ILRI Research Computing

about

anonymous@undisclosed.example.com (Anonymous) — Wed, 29 Nov 2017 13:18:45 +0000

About Agricultural research at ILRI and its partners are aimed at producing healthier crops and livestock to alleviate poverty and hunger in the developing world through exploitation of the latest genome technologies. These technologies require state-of-the-art high-performance computing infrastructure. A high performance computing (HPC) platform was established at ILRI to serve the Bioinformatics computing needs of ILRI - and central and eastern Africa researchers under the Biosciences East an…

abricate-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 08 Sep 2020 18:53:30 +0000

abricate Mass screening of contigs for antimicrobial resistance or virulence genes. It comes bundled with multiple databases: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB. Information * Version: 1.0.1 * Added: September, 2020

abyss-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 10 Jul 2019 14:25:33 +0000

Abyss Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler. Information * Version: 2.1.4 * Added: August, 2013 * Updated: November, 2018 * K-mer size: 128 (default at compile time) * Link: Usage See versions of abyss which are available:

ace-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 19 Nov 2025 12:28:06 +0000

ACE ACE corrects substitution errors in an Illumina archive using a k-mer trie. Information * Version: 1.01 * Added: February, 2019 * Max read length: 251 (default at compile time) * Link: Usage See versions which are available: $ module avail ace

act-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 23 May 2016 07:35:12 +0000

ACT Artemis Comparison Tool (ACT) is a Java application for displaying pairwise comparisons between two or more DNA sequences. Information * Version: 13.0.0 * Added: April, 2016 * Link: Usage See which versions of act are available: $ module avail act

adapterremoval-software

anonymous@undisclosed.example.com (Anonymous) — Sat, 22 Aug 2020 15:10:15 +0000

AdapterRemoval AdapterRemoval removes residual adapter sequences from next generation sequencing reads. The program handles both single end and paired end data. Information * Version: 2.3.1 * Added: September, 2014 * Updated: August, 2020 *

admixture-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 12 Jan 2016 06:31:33 +0000

ADMIXTURE ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm.

aegean-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 05 Feb 2018 11:29:04 +0000

AEGeAn Integrated toolkit for analysis and evaluation of annotated genomes. Information * Version: 0.16.0 * Added: February, 2018 * Link: Usage See versions of aegean which are available: $ module avail aegean Load one version into your environment:

aliview-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 05 Aug 2015 16:08:40 +0000

AliView AliView is yet another alignment viewer and editor, but this is probably one of the fastest and most intuitive to use, not so bloated and hopefully to your liking. Information * Version: 1.17.1 * Added: August, 2015 * Link: Usage

amber-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 23 Nov 2015 08:52:47 +0000

Amber Software Suite Amber Software suite consists of Amber & Amber Tools. AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.

amos

anonymous@undisclosed.example.com (Anonymous) — Thu, 22 Mar 2012 08:39:08 +0000

AMOS The AMOS source package has a name like: amos-3.1.0.tar.gz where 3.1.0 is the version of the code. Once you untar this file (using "tar -xzf amos-3.1.0.tar.gz" in Linux, or "gunzip -d amos-3.1.0.tar.gz | tar xf -" in other flavors of Unix) you will find the current AMOS distribution in a directory named amos-3.1.0. The next steps assume you have cd'd into this directory. AMOS uses the GNU autoconf package to reduce cross-platform compatibility issues. Before compiling the code you will nee…

ampssembler-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 15 Aug 2016 13:01:10 +0000

AMPssembler AMPssembler reconstitutes complete bar-coded cDNA transcripts from a mixture of sequenced libraries. Information * Version: git-51f0081 * Added: August, 2016 * Link: Usage See which versions of AMPssembler are available: $ module avail ampssembler

amrfinder-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 09 May 2025 15:50:27 +0000

AMRFinderPlus This software and the accompanying database identify acquired antimicrobial resistance genes in bacterial protein and/or assembled nucleotide sequences as well as known resistance-associated point mutations for several taxa. With AMRFinderPlus we added select members of additional classes of genes such as virulence factors, biocide, heat, acid, and metal resistance genes.

angsd-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 02 May 2017 18:53:58 +0000

ANGSD ANGSD(Analysis of Next Generation Sequencing Data) is a software for analyzing next generation sequencing data. Information * Version: 0.910 * Added: December, 2015 * Link: Usage See versions of angsd which are available: $ module avail angsd

annovar-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 09 Jun 2016 08:00:45 +0000

Annovar Annovar is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes. Information * Version: 2016-02-01 * Added: June, 2016 * Link: Usage See which versions of annovar are available:

ant-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 13 Feb 2017 12:15:53 +0000

Apache Ant Apache Ant is a Java library and command-line tool that help building software. Information * Version: 1.10.1 * Added: February, 2017 * Link: Usage See which versions of ant are available: $ module avail ant Load ant $ module load ant/1.10.1

antismash-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 11 May 2023 12:36:08 +0000

antismash The antiSMASH framework allows the detection of clusters of co-occurring biosynthesis genes in genomes, called Biosynthetic Gene Clusters (BGCs). BGCs often contain all the genes required for the biosynthesis of one or more Natural Products (NPs), also known as specialized or secondary metabolites. NPs show interesting biological activities and many of them have been developed into essential medicines, including antibiotics (penicillin, streptomycin), anti-cancer drugs (bleomycin, dox…

any2fasta-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 19 Aug 2020 19:06:11 +0000

any2fasta Convert various sequence formats to FASTA. Information * Version: 0.4.2 * Added: August, 2020 * Link: Usage See versions of any2fasta that are available: $ module avail any2fasta Load one version into your environment and run it:

apcupsd

anonymous@undisclosed.example.com (Anonymous) — Fri, 02 Sep 2011 12:42:44 +0000

APCUPSD The HPC's head node is connected to an APC battery backup unit which has a USB cable that can be used for monitoring power status. The APC UPS Daemon is configured on the server to monitor for power interuptions and notify the computer of the status. If power is off too long it can instruct the computer to shut down.

arb-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 13 Jan 2016 09:32:36 +0000

ARB ARB consists of various tools for sequence database handling and data analysis. Information * Version: 6.0.3 * Added: January, 2016 * Link: Usage See versions of arb which are available: $ module avail arb Load and run arb: $ module load arb/6.0.3 $ arb

artemis-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 20 Apr 2016 10:59:34 +0000

Artemis Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. Information * Version: 16.0.0

artic-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 24 Feb 2023 03:46:43 +0000

artic artic is a pipeline and set of accompanying tools for working with viral nanopore sequencing data, generated from tiling amplicon schemes. Information * Version: 1.2.3 * Added: February, 2023 * Link: Usage See versions which are available:

artic-tools-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 20 Feb 2023 08:02:32 +0000

artic-tools A set of tools for viral amplicon schemes: * download primer schemes and reference sequences * primer scheme validation * alignment softmasking * vcf filtering Information * Version: 0.3.1 * Added: February, 2023 * Link:

aspera-cli-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 18 Dec 2023 08:57:28 +0000

aspera-cli Command Line Interface for IBM Aspera products. Information * Version: 4.15.0 * Added: December, 2023 * Link: Usage See which versions are available: $ module avail aspera-cli Load one version into your environment and run it:

assembly-scan-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 13 May 2025 07:51:01 +0000

assembly-scan assembly-scan reads an assembly in FASTA format and outputs summary statistics in TSV or JSON format. Information * Version: 1.0.0 * Added: April, 2025 * Link: Usage See versions that are available: $ module avail assembly-scan

augur-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 15 Mar 2021 12:32:58 +0000

augur Augur is a bioinformatics toolkit to track evolution from sequence and serological data. It provides a collection of commands which are designed to be composable into larger processing pipelines. Augur originated as part of Nextstrain, an open-source project to harness the scientific and public health potential of pathogen genome data.

augustus-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 07 Jan 2018 15:40:30 +0000

Augustus Augustus predicts genes in eukaryotic genomic sequences. Information * Version: 3.3 * Added: January, 2018 * Link: Usage See which versions of augustus are available: $ module avail augustus Load one version into your environment:

awscli-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 22 Nov 2021 13:26:41 +0000

awscli This package provides a unified command line interface to Amazon Web Services. Information * Version: 2 (2.4.0) * Added: February, 2020 * Updated: November, 2021 * Link: Usage See which versions of awscli are available: $ module avail awscli

bam-readcount-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 23 May 2017 15:45:56 +0000

bam-readcount The purpose of this program is to generate metrics at single nucleotide positions. Information * Version: 0.8.0 * Added: May, 2017 * Link: Usage See which versions of bam-readcount are available: $ module avail bam-readcount

bamtools-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 26 Dec 2017 09:51:25 +0000

bamtools Bamtools provides C++ API & command-line toolkit for working with BAM data. Information * Version: 2.5.1 * Added: February, 2016 * Updated: December, 2017 * Link: Usage See which versions of bamtools are available: $ module avail bamtools

barrnap-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 29 Sep 2019 18:37:04 +0000

barrnap Barrnap predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), metazoan mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). It takes FASTA DNA sequence as input, and write GFF3 as output. It uses the new nhmmer tool that comes with HMMER 3.1 for HMM searching in RNA:DNA style. Multithreading is supported and one can expect roughly linear speed-ups with more CPUs.

basic_usage_of_grid_engine_commands

anonymous@undisclosed.example.com (Anonymous) — Sat, 22 May 2010 14:19:32 +0000

Basic Usage of Grid Engine qstat - Show job/queue status no arguments Show currently running/pending jobs -f Show full listing of all queues -j Shows detailed information on pending/running job -U Shows current jobs by user qhost - Show job/host status

bbmap-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 22 Feb 2022 13:34:58 +0000

BBMap BBMap is a splice-aware global aligner for DNA and RNA sequencing reads. It is part of the BBTools project and includes other tools like BBDuk. Information * Version: 38.95 * Added: September, 2019 * Updated: February, 2022 * Link:

bcftools-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 05 Dec 2025 07:28:41 +0000

bcftools BCFtools implements utilities for variant calling (in conjunction with SAMtools) and manipulating VCF and BCF files. The program is intended to replace the Perl-based tools from vcftools. Information * Latest Version: 1.22 * Added: September, 2015

beagle-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 21 Jun 2021 07:52:21 +0000

Beagle BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages such as BEAST. Information * Latest Version: 3.1.2 * Added: August, 2015 * Updated: June, 2021

beast-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 11 Nov 2019 15:46:26 +0000

BEAST BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. Information * Version: 1.10.4 * Added: August, 2014 * Updated: September, 2019 * Link: Usage See which versions of beast are available: $ module avail beast

beast2-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 21 Jun 2021 06:51:03 +0000

BEAST 2 BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. BEAST 2 is a complete re-write from the original BEAST. See the feature comparison table for more information. Information * Version: 2.6.4 * Added: June, 2021 *

bedops-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 01 Oct 2017 10:31:33 +0000

BEDOPS The fast, highly scalable and easily-parallelizable genome analysis toolkit. Information * Version: 2.4.29 * Added: September, 2017 * Link: Usage See which versions of bedops are available: $ module avail bedops Load a version of bedops into your environment:

bedtools-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 03 Mar 2025 07:38:43 +0000

bedtools Bedtools is a fast, flexible toolset for genome arithmetic. Information * Version: 2.31.1 * Added: January, 2013 * Updated: March, 2025 * Link: Usage See which versions of bedtools are available: $ module avail bedtools Load one version into your environment and run it:

binpacker-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 13 Feb 2017 07:43:30 +0000

BinPacker BinPacker - Serial Graph Partitioning and Fill-reducing Matrix Ordering. Information * Version: 1.0 * Added: January, 2017 * Link: Usage See which versions of BinPacker are available: $ module avail binpacker Load BinPacker $ module load binpacker/1.0

bio-linux

anonymous@undisclosed.example.com (Anonymous) — Sat, 22 May 2010 14:19:32 +0000

Bio-Linux Bio-Linux 5.0 is a fully featured, powerful, configurable and easy to maintain bioinformatics workstation. Bio-Linux provides more than 500 bioinformatics programs on an Ubuntu Linux base. There is a graphical menu for bioinformatics programs, as well as easy access to the Bio-Linux bioinformatics documentation system and sample data useful for testing programs. You can also install Bio-Linux packages to handle new generation sequence data type…

biological-databases

anonymous@undisclosed.example.com (Anonymous) — Mon, 09 Oct 2023 11:18:23 +0000

Biological Sequence Databases on the HPC Some of the most common biological sequence databases are available on the HPC for you to use with tools like BLAST. Below you can find the list of them, their location on the system, and the last time they were updated.

bioperl-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 06 Jun 2018 20:04:55 +0000

Perl The Bioperl Project is an international association of users & developers of open source Perl tools for bioinformatics, genomics and life science. Information * Version: 1.7.2 * Updated: December, 2017 * Link: Usage See which versions of bioperl are available:

bitseq-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 24 Mar 2016 13:33:56 +0000

BitSeq Transcript isoform level expression and differential expression estimation for RNA-seq. Information * Version: 0.7.5 * Added: March, 2016 * Link: Usage See which versions of bitseq are available: $ module avail bitseq Load bitseq

blasr-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 28 Sep 2017 15:10:06 +0000

blasr BLASR: The PacBio® long read aligner. Information * Version: smrtanalysis-4.0.0 * Added: September, 2017 * Link: Usage See versions of blasr which are available: $ module avail blasr Load one version into your environment: $ module load blasr/smrtanalysis-4.0.0

blast-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 24 Nov 2023 08:58:08 +0000

blast BLAST (Basic Local Alignment Search Tool) is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. A BLAST search enables a researcher to compare a query sequence with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain threshold.

blat-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 24 Jan 2023 08:29:09 +0000

blat BLAT performs extremely fast mRNA/DNA alignments, and cross-species protein alignments. Information * Version: 37x1 * Added: August, 2013 * Updated: January, 2023 * Link: Usage See versions of blat which are available: $ module avail blat

blobtools-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 18 Aug 2016 09:44:23 +0000

blobtools A python application for the visualization of draft genome assemblies and general QC. Information * Version: 0.9.19.3 * Added: August, 2016 * Link: Usage See which versions of blobtools are available: $ module avail blobtools

bmtagger-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 23 Mar 2022 07:55:04 +0000

bmtagger Best Match Tagger for removing human reads from metagenomics datasets. Information * Version: 0.3.102.4 * Added: March, 2022 * Link: Usage See versions which are available: $ module avail bmtagger Load one version into your environment and run it:

bowtie-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 27 Apr 2020 11:13:48 +0000

Bowtie Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2

bowtie1-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 17 Oct 2014 07:47:39 +0000

Bowtie * Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2

bowtie2-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 03 Mar 2025 07:29:17 +0000

Bowtie 2 Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2

brainstorms

anonymous@undisclosed.example.com (Anonymous) — Fri, 06 Sep 2013 09:40:50 +0000

Brainstorming Notes from various brainstorming sessions. Policy, infrastructure, and the way forward™. For all eyes! 2012 * research_computing_storage_infrastructure_2012

brig-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 16 Sep 2015 09:32:57 +0000

BRIG BLAST Ring Image Generator(BRIG) displays circular comparisons between a large number of genomes, with a focus on handling genome assembly data. Information * Version: 0.95 * Added: September, 2015 * Link: Usage See versions of BRIG which are available:

bt03srv

anonymous@undisclosed.example.com (Anonymous) — Fri, 09 Sep 2022 11:50:14 +0000

bt03srv 2022-09-09: Decommissioned by Steve Kemp. Provisioned with a basic Ubuntu 14.04 system. After provisioning RAID was set up like this: # apt-get install mdadm # mdadm -E /dev/sd[a-d] mdadm: No md superblock detected on /dev/sda. mdadm: No md superblock detected on /dev/sdb. mdadm: No md superblock detected on /dev/sdc. mdadm: No md superblock detected on /dev/sdd. # mdadm --create /dev/md0 --level=10 --raid-devices=4 /dev/sd[a-d] mdadm: Defaulting to version 1.2 metadata mdadm: array /…

busco-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 21 Mar 2023 12:37:37 +0000

BUSCO BUSCO (Benchmarking Universal Single-Copy Orthologs) assesses genome assembly and annotation completeness with single-copy ortholog. Information * Latest Version: 5.2.2 * Added: August, 2015 * Updated: December, 2021 * Link: Usage

bwa-mem2-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 05 Sep 2024 12:36:01 +0000

Burrows-Wheeler Aligner bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. The original bwa was developed by Heng Li (@lh3). Performance enhancement in bwa-mem2 was primarily done by Vasimuddin Md (@yuk12) and Sanchit Misra (@sanchit-misra) from Parallel Computing Lab, Intel. bwa-mem2 is distributed under the MIT license.

bwa-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 13 May 2025 08:01:03 +0000

Burrows-Wheeler Aligner BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. Information * Latest version: 0.7.19 * Added: April, 2013 * Updated: May, 2025 * Link: Usage

cafe-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 12 Jun 2018 15:09:28 +0000

cafe The purpose of CAFE is to analyze changes in gene family size in a way that accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences. Information * Version: 4.1 * Added: June, 2018 * Link: Usage

canu-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 14 Feb 2019 09:52:36 +0000

Canu Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). Information * Version: 1.8 * Added: September, 2017 * Updated: October, 2018 * Link: Usage

ccmetagen-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 14 Mar 2022 13:15:45 +0000

ccmetagen Microbiome classification pipeline. Information * Version: 1.4.0 * Added: March, 2022 * Link: Usage See which versions are available: $ module avail ccmetagen Load one version into your environment and run it: $ module load ccmetagen/1.4.0 $ CCMetagen.py

cd-hit-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 17 Mar 2021 13:19:43 +0000

CD-HIT A program for clustering and comparing protein or nucleotide sequences. Information * Version: 4.8.1 * Added: August, 2016 * Updated: March, 2021 * Link: Usage See which versions of cd-hit are available: $ module avail cd-hit Load one version into your environment and run it:

cegma-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 29 Jul 2015 07:41:28 +0000

CEGMA CEGMA (Core Eukaryotic Genes Mapping Approach) is a software package for building a highly reliable set of gene annotations in the absence of experimental data. Information * Version: v2.5 * Added: November, 2014 * Link: Usage See versions of cegma which are available

centrifuge-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 13 Jul 2022 18:23:50 +0000

centrifuge Centrifuge is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples, with better sensitivity than and comparable accuracy to other leading systems. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem.

cgmlst-dists-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 11 Oct 2023 08:09:25 +0000

cgmlst-dists Calculate distance matrix from cgMLST allele call tables of ChewBBACA. Information * Version: 0.4.0 * Added: October, 2023 * Link: Usage See which versions are available: $ module avail cgmlst-dists Load one version into your environment and run it:

chado

anonymous@undisclosed.example.com (Anonymous) — Sat, 22 May 2010 14:19:32 +0000

Chado Create new T.pava Chr1 Chado database from Chr1 Genbank file. Local version of Genbank file does not work. Downloaded new file from Genbank: NC_001142.gbk Convert file to gff using script: bp_genbank2gff3.pl NC_001142.gbk Create pgsql database.

changeo-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 25 Apr 2022 15:14:10 +0000

Change-O Change-O is a collection of tools for processing the output of V(D)J alignment tools, assigning clonal clusters to immunoglobulin sequences, and reconstructing germline sequences. Information * Version: 1.2.0 * Added: September, 2016

checkm-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 12 Mar 2020 16:45:18 +0000

CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. It provides robust estimates of genome completeness and contamination by using collocated sets of genes that are ubiquitous and single-copy within a phylogenetic lineage.

chewbbaca-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 28 Sep 2023 09:59:17 +0000

chewbbaca chewBBACA is a comprehensive pipeline including a set of functions for the creation and validation of whole genome and core genome MultiLocus Sequence Typing (wg/cgMLST) schemas, providing an allele calling algorithm based on Blast Score Ratio that can be run in multiprocessor settings and a set of functions to visualize and validate allele variation in the loci. chewBBACA performs the schema creation and allele calls on complete or draft genomes.

circos-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 28 Nov 2022 08:10:54 +0000

Circos Circos is a software package for visualizing data and information a circular layout. Information * Version: 0.69-9 * Added: July, 2014 * Updated: November, 2022 * Link: Usage See versions which are available: $ module avail circos

clonalframe-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 16 Sep 2015 09:54:50 +0000

ClonalFrame ClonalFrame infers bacterial microevolution using multilocus sequence data. Information * Version: 1.2 * Added: September, 2015 * Link: Usage See versions of ClonalFrame which are available: $ module avail clonalframe Load and run ClonalFrame:

clonalframeml-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 20 Nov 2015 07:30:04 +0000

ClonalFrameML ClonalFrameML performs efficient inference of recombination in bacterial genomes. Information * Version: 1.0 * Added: November, 2015 * Link: Usage See versions of ClonalFrameML which are available: $ module avail clonalframeml

cnvnator-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 25 May 2017 16:13:15 +0000

CNVnator A tool for CNV discovery and genotyping from depth-of-coverage by mapped reads. Information * Version: 0.3.3 * Added: May, 2017 * Link: Usage See versions of CNVnator which are available: $ module avail root Load and run root:

commands

anonymous@undisclosed.example.com (Anonymous) — Sat, 22 May 2010 14:19:32 +0000

Useful commands List node activity from command line gstat --all Add a new user On the head node, create the user account: # /usr/sbin/adduser jsmith Change the user's password: # passwd jsmith Sync the changes to disk (Rocks updates autofs and sends config files to compute nodes):

configuring-key-based-ssh-authentication

anonymous@undisclosed.example.com (Anonymous) — Fri, 06 Jan 2023 07:03:40 +0000

Configuring Key-Based SSH Authentication As of 2023 we no longer allow password authentication to the ILRI, Nairobi HPC. All users must use SSH keys instead. This is due to the increasingly hostile nature of the public Internet, where malicious bots constantly barrage publicly accessible servers with login attempts, hoping to get lucky.

cooler-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 11 Nov 2020 08:46:06 +0000

cooler Cooler is a support library for a sparse, compressed, binary persistent storage format, also called cooler, used to store genomic interaction data, such as Hi-C contact matrices. Information * Version: 0.8.10 * Added: November, 2020 *

coperead-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 08 Feb 2017 13:49:43 +0000

COPEread COPE (Connecting Overlapped Pair-End reads) is a method to align and connect the illumina sequenced Pair-End reads of which the insert size is smaller than the sum of the two read length. Information * Latest Version: 1.1.2 * Added: February, 2017

corset-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 03 Nov 2016 12:34:53 +0000

corset Corset is a software for clustering de novo assembled transcripts and counting overlapping reads Information * Latest Version: 1.06 * Added: November, 2016 * Link: Usage See which versions of corset are available: $ module avail corset

crispresso2-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 27 Jun 2025 13:46:48 +0000

CRISPResso2 CRISPResso2 is a software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments. Information * Version: 2.3.2 * Added: June, 2025 * Link: Usage See which versions are available: $ module avail crispresso2

cutadapt-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 30 Apr 2025 09:01:32 +0000

cutadapt Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Information * Version: 5.0 * Added: June, 2015 * Updated: April, 2025 * Link: Usage

cytoscape-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 07 Oct 2024 06:38:06 +0000

cytoscape Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization.

czid-cli-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 24 Feb 2022 06:57:18 +0000

czid-cli A Command Line Interface for CZ ID (formerly known as idseq-cli). Information * Version: 3.0.2 * Added: February, 2022 * Link: Usage See which versions of czid-cli are available: $ module avail czid-cli Load one version into your environment and run it:

database

anonymous@undisclosed.example.com (Anonymous) — Wed, 23 Jun 2010 17:38:56 +0000

Database * MySQL * PostgreSQL

dextractor-software

anonymous@undisclosed.example.com (Anonymous) — Sat, 10 Nov 2018 16:08:38 +0000

dextractor Bax File Decoder and Data Compressor. Information * Version: git-a7f50c52 (developer does not tag proper release versions) * Added: November, 2018 * Link: Usage See versions of dextractor which are available: $ module avail dextractor

diamond-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 17 Mar 2022 09:10:18 +0000

Diamond Diamond is a new high-throughput program for aligning DNA reads or protein sequences against a protein reference database such as NR, at up to 20,000 times the speed of BLAST, with high sensitivity. Information * Version: 2.0.14 * Added: November, 2016

diskutil

anonymous@undisclosed.example.com (Anonymous) — Sat, 22 May 2010 14:19:32 +0000

Create Bootable Live USB Drives using Diskutil (MacOSX) * Download the desired .img file * Open a Terminal (under Utilities) * Run diskutil list to get the current list of devices * Insert your flash media * Run diskutil list again and determine the device node assigned to your flash media (e.g.

disty-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 13 Sep 2023 06:08:02 +0000

disty Compute a distance matrix from a core genome alignment file. Information * Version: 0.1.0 * Added: September, 2023 * Link: Usage See which versions are available: $ module avail disty Load one version into your environment and run it:

diy

anonymous@undisclosed.example.com (Anonymous) — Sat, 22 May 2010 14:19:32 +0000

DIYA:: (currently works on HPC head node only) ---------- DIYA (Do-It-Yourself Annotator) is a modular and configurable open source pipeline framework, written in Perl, used for the rapid annotation of microbial genome sequences. The software is currently used to take nucleotide sequence contigs as input, either in the form of complete genomes or the result of shotgun sequencing, and produce an annotated sequence.

dnaapler-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 13 May 2025 09:52:15 +0000

dnaapler Dnaapler is a simple tool that reorients complete circular microbial genomes. Information * Version: 1.2.0 * Added: March, 2025 * Link: Usage See versions that are available: $ module avail dnaapler Load one version into your environment and run it:

dorado-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 09 Apr 2026 08:49:56 +0000

dorado Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. Information * Version: 1.4.0 * Added: September, 2023 * Updated: April, 2026 * Link: Usage See which versions are available: $ module avail dorado

dragonflye-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 13 May 2025 13:41:20 +0000

dragonflye Assemble bacterial isolate genomes from Nanopore reads. Information * Version: 1.2.1 * Added: May, 2025 * Link: Usage See which versions are available: $ module avail dragonflye Load one version into your environment and run it:

drep-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 12 Mar 2020 14:21:22 +0000

drep dRep is a python program for rapidly comparing large numbers of genomes. dRep can also "de-replicate" a genome set by identifying groups of highly similar genomes and choosing the best representative genome for each genome set. Information *

ea-utils-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 18 Nov 2018 09:14:18 +0000

ea-utils Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs. Information * Version: 1.04.807 * Added: October, 2015

eagle-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 17 Jun 2022 07:14:43 +0000

eagle The Eagle software estimates haplotype phase either within a genotyped cohort or using a phased reference panel. Eagle2 is now the default phasing method used by the Sanger and Michigan imputation servers and uses a new, very fast HMM-based algorithm that improves speed and accuracy over existing methods via two key ideas: a new data structure based on the positional Burrows-Wheeler transform and a rapid search algorithm that explores only the most relevant paths through the HMM. Compared…

easer-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 23 May 2016 07:35:52 +0000

EASER EASER(Ensembl Easy Sequence Retriever) is a python program based in PyCogent library for the homology-based retrieval of several sequence data types from Ensembl. Information * Version: 1.7.0 * Added: May, 2016 * Link: Usage See which versions of easer are available:

ectyper-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 24 Aug 2025 10:02:35 +0000

ectyper ECTyper is a standalone versatile serotyping module for Escherichia coli. It supports both fasta (assembled) and fastq (raw reads) file formats. The tool provides convenient species identification coupled to quality control module giving a complete, transparent and reference laboratories suitable report on E.coli serotyping, Shiga toxin typing and pathotyping.

edirect-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 30 Jan 2018 09:45:16 +0000

EDirect EDirect is a software package, developed by NCBI, which allows you to use the E-utilities API in a Unix environment. It helps you quickly and easily use the E-utilities API, and has built-in tools to extract specific data from XML files and create tables of data that can be more easily analyzed or visualized.

eggnog-mapper-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 27 Sep 2022 08:01:26 +0000

eggNOG mapper EggNOG-mapper (a.k.a. emapper.py or just emapper) is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups (OGs) and phylogenies from the eggNOG database () to transfer functional information from fine-grained orthologs only.

emblmygff3-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 17 May 2022 07:09:05 +0000

EMBLmyGFF3 An efficient way to convert gff3 annotation files into EMBL format ready to submit. Information * Version: 2.1 * Added: May, 2022 * Link: Usage See versions which are available: $ module avail emblmygff3 Load one version into your environment and run it:

emboss-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 24 Dec 2017 14:08:02 +0000

EMBOSS Information * Version: 6.6.0 * Added: November, 2013 * Link: Usage See versions of emboss which are available: $ module avail emboss Load one version into your environment: $ module load emboss/6.6.0 Installation Notes from the sysadmin during installation:

enable_nagios_commands_via_web-interface

anonymous@undisclosed.example.com (Anonymous) — Tue, 05 Jun 2012 11:54:53 +0000

In the /etc/nagios3/nagios.cfg file, make sure you have similar values: check_external_commands=1 command_check_interval=15s command_file=/var/lib/nagios3/rw/nagios.cmd Add www-data user to nagios group usermod www-data -G nagios dpkg-statoverride --update --add nagios www-data 2710 /var/lib/nagios3/rw dpkg-statoverride --update --add nagios nagios 751 /var/lib/nagios

epel

anonymous@undisclosed.example.com (Anonymous) — Sat, 22 May 2010 14:19:32 +0000

Extra Packages for Enterprise Linux EPEL is a community-driven, Redhat-backed repository for use with Enterprise Linux (and therefore CentOS, Rocks, etc). It provides many useful packages not provided by the official repositories while maintaining compatibility with upstream releases.

ergatis

anonymous@undisclosed.example.com (Anonymous) — Sat, 22 May 2010 14:19:32 +0000

Ergatis Ergatis is a web-based utility that is used to create, run, and monitor reusable computational analysis pipelines. It contains pre-built components for common bioinformatics analysis tasks. These components can be arranged graphically to form highly-configurable pipelines. Each analysis component supports multiple output formats, including the Bioinformatic Sequence Markup Language (BSML). The current implementation includes support for data loading into project databases following the

ete-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 14 Mar 2022 08:58:43 +0000

ete Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree. Information * Version: 3.1.2

exabayes-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 12 Feb 2016 06:39:50 +0000

Exabayes ExaBayes is a software package for Bayesian tree inference. It is particularly suitable for large-scale analyses on computer clusters. Information * Version: 1.4.1 * Added: February, 2016 * Link: Usage See which versions of exabayes are available:

express-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 02 Nov 2015 11:36:12 +0000

eXpress eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. Information * Version: 1.5.1 * Added: November, 2015 * Link: Usage See versions of eXpress which are available: $ module avail express

ezclermont-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 25 Aug 2025 09:37:31 +0000

ezclermont This is a tool for using the Clermont 2013 PCR typing method for in silico analysis of E. coli whole genomes or assembled contigs. Information * Version: 0.7.0 * Added: August, 2025 * Link: Usage See which versions are available:

falco-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 07 Apr 2022 06:34:36 +0000

falco A C++ implementation of FastQC for quality control of sequencing data. Information * Version: 0.3.0 * Added: March, 2022 * Link: Usage See versions that are available: $ module avail falco Load one version into your environment and run it:

falcon-phase-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 11 Nov 2020 15:37:01 +0000

FALCON-Phase FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds. Information * Version: git-7c50154e * Added: November, 2020 * Link: Usage See which versions of falcon-phase are available:

faq

anonymous@undisclosed.example.com (Anonymous) — Wed, 06 Mar 2019 14:30:43 +0000

Frequently Asked Questions How many CPUs can I use? By default everyone is allowed to use 20 CPUs or 20 jobs (whichever limit you hit first). How do I get an interactive shell with SLURM? Use the command interactive, which will request 1 CPU on a free compute node for an interactive session. Use

fastani-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 03 May 2020 14:32:03 +0000

fastANI FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.

fastp-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 13 May 2025 10:17:52 +0000

fastp A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. Information * Version: 0.24.1 * Added: May, 2025 * Link: Usage See versions that are available:

fastphase-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 03 Jul 2017 11:08:14 +0000

fastPHASE fastPHASE is a program to estimate missing genotypes and unobserved haplotypes. Information * Latest version: 1.4.8 * Added: July, 2017 * Link: Usage See versions of fastPHASE which are available: $ module avail fastPHASE Load and run:

fastq-demux-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 27 Jun 2025 09:47:36 +0000

FASTQ demux A simple program to demultiplex Illumina FASTQ files based on barcodes in the FASTQ headers. Information * Version: git-dff5823f * Added: June, 2025 * Link: Usage See available versions: $ module avail fastq_demux Load one version into your environment and run it:

fastq-scan-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 28 Apr 2025 13:02:17 +0000

fastq-scan fastq-scan reads a FASTQ from STDIN and outputs summary statistics (read lengths, per-read qualities, per-base qualities) in JSON format. Information * Version: 1.0.1 * Added: April, 2025 * Link: Usage See versions that are available:

fastqc-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 15 Dec 2021 07:39:55 +0000

fastqc A quality control tool for high throughput sequence data. Information * Latest version: 0.11.9 * Added: December, 2014 * Updated: December, 2021 * Link: Usage See versions of fastqc which are available: $ module avail fastqc Load one version into your environment and run it:

faststructure-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 17 Feb 2017 14:30:01 +0000

fastStructure fastStructure is an algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x. Information * Version: 1.0 * Added: May, 2014

fasttree-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 09 Aug 2020 12:52:48 +0000

FastTree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. For large alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or RAxML 7.

fastx-toolkit-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 05 Dec 2014 14:08:15 +0000

fastx_toolkit FASTQ/A short-reads pre-processing tools. Information * Version: 0.0.13 * Added: May 27, 2014 * Link: Usage See versions which are available module avail fastx_toolkit Installation Notes from the sysadmin during installation:

figaro-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 05 Sep 2023 07:23:09 +0000

figaro FIGARO will quickly analyze error rates in a directory of FASTQ files to determine optimal trimming parameters for high-resolution targeted microbiome sequencing pipelines, such as those utilizing DADA2 and Deblur. The mission of this application is identical to the ZymoBIOMICS mission: increasing the reproducibility and standardization of microbiome analysis.

firefox-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 02 Dec 2014 06:33:52 +0000

Firefox Firefox is a web browser by Mozilla. v33.1.1 * Version: 33.1.1 * Added: November, 2014 * Link: Usage * Show all available versions of firefox module avail firefox * Load firefox module: module load firefox/33.1.1 * get quick help:

flapjack-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 24 Apr 2018 07:46:32 +0000

Flapjack Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data, allowing for rapid navigation and comparisons between lines, markers and chromosomes. Information * Version: 1.18.04.23-beta

flash-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 20 Sep 2017 13:29:41 +0000

FLASH FLASH, Fast Length Adjustment of SHort reads, is a very accurate fast tool to merge paired-end reads from fragments that are shorter than twice the length of reads. The extended length of reads has a significant positive impact on improvement of genome assemblies.

flash2-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 20 Sep 2017 13:31:28 +0000

FLASH2 FLASH, Fast Length Adjustment of SHort reads, is a very accurate fast tool to merge paired-end reads from fragments that are shorter than twice the length of reads. The extended length of reads has a significant positive impact on improvement of genome assemblies.

flexbar-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 16 May 2016 13:02:40 +0000

Flexbar flexbar is a flexible barcode and adapter processing for next-generation sequencing platforms. Information * Version: 2.7.0 * Added: May, 2016 * Link: Usage See which versions of flexbar are available: $ module avail flexbar Load flexbar

flux-capacitor-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 24 Mar 2016 13:39:39 +0000

Flux Capacitor Flux Capacitor predicts abundances for transcript molecules and alternative splicing events from RNAseq experiments. Information * Version: 1.6.1 * Added: March, 2016 * Link: Usage See which versions of flux-capacitor are available:

flye-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 14 May 2025 06:49:56 +0000

Flye Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Flye also includes a special mode for metagenome assembly.

form_tools

anonymous@undisclosed.example.com (Anonymous) — Sat, 22 May 2010 14:19:32 +0000

Form Tools Form Tools is an online registration site. Put simply, it is a form processor, storage and data access script written in PHP and MySQL, designed to work with any existing web form. With a few minor changes to your form, you can stop using old-fashioned form-mail scripts and instead store form submissions in a database, instantly providing your clients with a user-friendly interface to manage their form submissions, include options such as mass data export via Excel, printer-friendly …

fraggenescan-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 15 Mar 2020 09:17:24 +0000

FragGeneScan FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes. Information * Version: 1.30 * Added: July, 2015 * Updated: March, 2020

freebayes-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 11 Aug 2021 09:20:56 +0000

FreeBayes Bayesian haplotype-based polymorphism discovery and genotyping Information * Version: 1.3.4 * Added: August, 2021 * Link: Usage See which versions of freebayes are available: $ module avail freebayes Load one version into your environment and run it:

freebsd

anonymous@undisclosed.example.com (Anonymous) — Sat, 22 May 2010 14:19:32 +0000

keep ports up to date $portsnap fetch

funannotate-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 20 Apr 2023 21:21:34 +0000

funannotate funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Information * Version: 1.8.15 * Added: August, 2021 * Updated: April, 2023 * Link: Usage Funannotate is installed in a dedicated "container" environment using

gaas

anonymous@undisclosed.example.com (Anonymous) — Sat, 22 May 2010 14:19:32 +0000

GAAS ---------- GAAS (Genome relative Abundance and Average Size) is a bioinformatic tool to calculate accurate community composition and average genome size in metagenomes by using BLAST, advanced parsing of hits and correction of genome length bias.

gambit-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 20 Nov 2025 06:54:21 +0000

gambit GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking) is a tool for rapid taxonomic identification of microbial pathogens. It uses an efficient genomic distance metric along with a curated database of approximately 50,000 reference genomes (derived from NCBI RefSeq) to identify genome assemblies from across the Bacterial kingdom in seconds.

gapfiller-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 17 Nov 2016 07:21:05 +0000

GapFiller GapFiller is a stand-alone program for closing gaps within pre-assembled scaffolds. Information * Latest Version: 1.10 * Added: November, 2016 * Link: Usage See which versions of gapfiller are available: $ module avail gapfiller

gassflow-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 22 Feb 2017 14:20:21 +0000

GassFlow GassFlow(Genome Annotation based on Species Similarity) is a computational tool to annotate a eukaryotic genome based on only the annotations from another similar species. Information * Version: 1.0 * Added: February, 2017 * Link:

gatk-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 09 Jan 2026 09:46:25 +0000

Genome Analysis ToolKit (GATK) GATK offers a wide variety of tools with a primary focus on variant discovery and genotyping. Information * Latest Version: 4.4.0.0 * Added: May, 2014 * Updated: May, 2023 * Link: Usage See which versions are available:

geneid-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 07 Nov 2014 17:26:37 +0000

geneid geneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. Information * Version: 1.4.4 * Added: November, 2014 * Link: Usage See versions of geneid which are available module avail geneid

genome_assemblers

anonymous@undisclosed.example.com (Anonymous) — Wed, 30 Jun 2010 18:00:11 +0000

Genome Assemblers * MIRA * Celera WGS * Newbler

genometools-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 09 Nov 2020 07:43:08 +0000

GenomeTools The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. Information * Version: 1.6.1 * Added: November, 2020 * Link: Usage

genomeworks-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 20 Sep 2021 07:44:48 +0000

genomeworks SDK for GPU accelerated genome assembly and analysis. Information * Version: git-baab5668 * Added: September, 2021 * Link: Usage See versions of genomeworks that are available: $ module avail genomeworks Load one version into your environment and run it:

genscan-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 17 Feb 2016 05:56:45 +0000

Genscan Genscan predicts genes in eukaryotic genomic sequences. Information * Version: latest * Added: February, 2016 * Link: Usage See which versions of genscan are available: $ module avail genscan Load genscan $ module load genscan/latest

genvar

anonymous@undisclosed.example.com (Anonymous) — Sat, 22 May 2010 14:19:32 +0000

GenVar ---------- The pipeline, based on the program GeneWise, is designed to analyze an annotated genome and automatically identify missed gene calls and sequence variants such as genes with disrupted reading frames (split genes) and those with insertions and deletions (indels). For a given genome to be analyzed, GenVar relies on a database containing closely related genomes (such as other species or strains) as well as a few additional reference genomes. GenVar also helps identify gene disru…

gffread-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 13 Feb 2017 12:02:34 +0000

GFFRead GFFRead is a GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction. Information * Version: 0.9.6 * Added: February, 2017 * Link: Usage See which versions of gffread are available: $ module avail gffread

gmap-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 24 Mar 2016 13:40:24 +0000

GMAP-GSNAP A Genomic Mapping and Alignment Program(GMAP) for mRNA and EST Sequences and Genomic Short-read Nucleotide Alignment Program(GSNAP). Information * Version: 2015-12-31 * Added: March, 2016 * Link: Usage See which versions of gmap are available:

gofasta-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 21 May 2025 07:32:48 +0000

gofasta gofasta is a command-line utility developed to handle SARS-CoV-2 alignments, but should be useful more generally for handling consensus genomes of any microbial pathogen. It has been used on datasets of millions of sequences, including by the United Kingdom's daily SARS-CoV-2 genome processing pipelines, Pangolin and Civet.

graphlan-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 10 Mar 2022 12:20:49 +0000

graphlan GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. Information * Version: 1.1.3 * Added: March, 2022 * Link: Usage See which versions are available: $ module avail graphlan

graphmap-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 04 Nov 2018 16:05:43 +0000

graphmap A highly sensitive and accurate mapper for long, error-prone reads. Information * Latest version: 0.5.2 * Added: November, 2018 * Link: Usage See versions of graphmap that are available: $ module avail graphmap Load one version into your environment and run it:

grom-rd-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 24 May 2017 08:33:42 +0000

GROM-RD Analyzes multiple biases in read coverage to detect CNVs in NGS data. To overcome a typical weakness of read depth (RD) methods, GROM-RD employs a CNV search using size-varying overlapping windows to improve breakpoint resolution. GROM-RD was able to improve RD sensitivity, specificity, and breakpoint accuracy compared to CNVnator and RDXplorer, the two most frequently used RD algorithms. Additionally, GROM-RD had a short run time that was relatively insensitive to read coverage indicat…

gromacs-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 11 Nov 2019 14:48:33 +0000

Gromacs GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. Information * Version: 2018.2 * Added: July, 2018 * Link: Usage See versions of gromacs which are available:

groovy-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 14 Mar 2017 13:47:09 +0000

Groovy Apache Groovy is a powerful, optionally typed and dynamic language, with static-typing and static compilation capabilities, for the Java platform aimed at improving developer productivity thanks to a concise, familiar and easy to learn syntax.

gsea-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 06 Feb 2017 06:54:47 +0000

Gene Set Enrichment Analysis(GSEA) Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states(e.g. phenotypes).

gtdbtk-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 04 May 2020 20:25:30 +0000

gtdbtk GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes.

gubbins-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 15 May 2025 08:27:35 +0000

gubbins Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions, which are marked as recombinations, while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours…

guidance-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 22 Nov 2016 19:02:02 +0000

Guidance Guidance is a tool for multiple sequence alignment. Information * Latest Version: 2.02 * Added: November, 2016 * Link: Usage See which versions of guidance are available: $ module avail guidance Load pagan $ module load guidance/2.02

guppy-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 06 Dec 2023 06:42:47 +0000

guppy Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies' basecalling algorithms, and several bioinformatic post-processing features. See this tutorial: Information * Version: 6.5.7 * Added: July, 2021 * Updated: December, 2023

halcyon-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 19 Aug 2021 10:28:10 +0000

halcyon An accurate basecaller exploiting an encoder-decoder model with monotonic attention. Information * Version: 0.1.1 (note that the version on GitHub and PyPi doesn't match) * Added: August, 2021 * Link: Usage See which versions of halcyon are available: $ module avail halcyon

hapflk-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 24 Oct 2017 11:53:38 +0000

hapflk hapflk is a software implementing the hapFLK and FLK tests for the detection of selection signatures based on multiple population genotyping data. Information * Version: 1.4 * Added: October, 2017 * Link: Usage See versions of hapflk which are available:

hawk-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 16 Feb 2022 14:21:55 +0000

hawk Hitting associations with k-mers. Information * Version: git-a177811d (~1.7.0) * Added: February, 2022 * Link: Usage See versions of hawk that are available: $ module avail hawk Load one version into your environment and run it: $ module load hawk/git-a177811d $ hawk

hclust2-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 07 Sep 2021 14:35:00 +0000

hclust2 Hclust2 is a handy tool for plotting heat-maps with several useful options to produce high quality figures that can be used in publication. Information * Version: 1.0.0 * Added: September, 2021 * Link: Usage See which versions of hclust2 are available:

hdf5-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 28 Sep 2017 10:35:05 +0000

HDF5 HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. The HDF5 Technology suite includes tools and applications for managing, manipulating, viewing, and analyzing data in the HDF5 format.

hic_qc-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 09 Nov 2020 09:53:32 +0000

hic_qc This script is intended as a simple QC method for Hi-C libraries, based on reads in a BAM file aligned to some genome/assembly. Information * Version: git-1e132fb2 * Added: November, 2020 * Link: Usage See versions of hic_qc that are available:

hifiasm-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 18 May 2022 07:43:07 +0000

hifiasm A haplotype-resolved assembler for accurate Hifi reads. Information * Version: 0.16.1 * Added: March, 2022 * Link: Usage See which versions are available: $ module avail hifiasm Load one version into your environment and run it:

hisat2-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 27 Sep 2018 14:08:37 +0000

HISAT2 HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads to a population of human genomes. Information * Latest Version: 2.1.0 * Added: September, 2018 * Link: Usage See available versions of hisat2:

hmmer-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 15 Mar 2020 16:39:33 +0000

HMMER HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Information * Version: 3.3 * Added: September, 2017

hmmibd-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 05 May 2021 13:08:30 +0000

hmmIBD A hidden Markov model for detecting segments of shared ancestry (identity by descent) in genetic sequence data. Information * Version: 2.0.4 * Added: May, 2021 * Link: Usage See which versions of hmmIBD are available: $ module avail hmmIBD

hostile-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 03 Mar 2025 07:57:05 +0000

hostile Hostile accurately removes host sequences from short and long read (meta)genomes, consuming single or paired FASTQ from files or stdin. Batteries are included – a human reference genome is downloaded when run for the first time. Hostile is precise by default, removing an order of magnitude fewer microbial reads than existing approaches while removing >99.5% of real human reads from 1000 Genomes Project samples.

how_to_setup_check_megaraid_sas

anonymous@undisclosed.example.com (Anonymous) — Wed, 04 Apr 2012 09:07:17 +0000

How to setup check_megaraid_sas 1. Make sure you have Megacli installed. In HPC it's installed in /opt/MegaRAID/MegaCli/ 2. Download check_megaraid_sas script from Nagios Exchange to the plugins folder of the host. In most systems this is in /usr/lib64/nagios/plugins or /usr/lib/nagios/plugins

hpc_concepts

anonymous@undisclosed.example.com (Anonymous) — Sat, 22 May 2010 14:19:32 +0000

Message Passing Interface (MPI): The Concept ---------- The MPI interface is meant to provide essential virtual topology, synchronization, and communication functionality between a set of processes (that have been mapped to nodes/servers/computer instances) in a language-independent way, with language-specific syntax (bindings), plus a few features that are language-specific. MPI programs always work with processes, but programmers commonly refer to the processes as processors. Typically, for …

hpc-users-group

anonymous@undisclosed.example.com (Anonymous) — Wed, 13 Mar 2019 20:04:37 +0000

HPC Users Group The HPC Users Group was an informal gathering of users of the ILRI, Nairobi high-performance computing platform. Topics discussed included: * HPC infrastructure organization * Job scheduling * Linux scripting * Cluster best practices

hpg-variant-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 02 Apr 2015 13:20:06 +0000

HPG Variant HPG Variant is a tool for fast, memory-efficient counting of k-mers in DNA Information * Version: 1.0 * Added: April, 2015 * Link: Usage See versions of hpg-variant which are available $ module avail hpg-variant Load and run hpg-variant

htseq-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 20 Sep 2017 12:15:21 +0000

htseq A framework to process and analyze data from high-throughput sequencing (HTS) assays. Information * Version: 0.9.1 * Added: October, 2013 * Updated: September, 2017 * Link: Usage See versions of htseq which are available: $ module avail htseq

htslib-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 05 Dec 2025 06:40:52 +0000

htslib htslib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools Information * Latest Version: 1.22.1

hyphy-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 02 Mar 2023 11:14:59 +0000

hyphy HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning.

hypo-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 06 Jan 2021 15:31:50 +0000

hypo HyPo--a Hybrid Polisher-- utilises short as well as long reads within a single run to polish a long reads assembly of small and large genomes. It exploits unique genomic kmers to selectively polish segments of contigs using partial order alignment of selective read-segments. As demonstrated on human genome assemblies, Hypo generates significantly more accurate polished assembly in about one-third time with about half the memory requirements in comparison to contemporary widely used polishe…

idba-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 15 Mar 2020 10:44:40 +0000

IDBA IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. Information * Version: 1.1.2 * Added: March, 2020 * Link: Usage See versions of idba which are available:

idea

anonymous@undisclosed.example.com (Anonymous) — Sat, 22 May 2010 14:19:32 +0000

Interactive Display for Evolutionary Analyses IDEA (Interactive Display for Evolutionary Analyses) is a graphical interface for PAML (Yang, Z., 1997), a popular package for conducting molecular evolution analyses on phylogenies and associated sequences.

igblast-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 16 Apr 2020 13:43:27 +0000

IgBLAST IgBLAST was developed at NCBI to facilitate analysis of immunoglobulin variable domain sequences but has recently been extended to perform analysis for T cell receptor (TR) sequences. Information * Version: 1.10.0 * Added: September, 2016

igdiscover-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 16 Apr 2020 14:38:37 +0000

IgDiscover IgDiscover analyzes antibody repertoires and discovers new V genes from high-throughput sequencing reads. Heavy chains, kappa and lambda light chains are supported (to discover VH, VK and VL genes). Information * Version: 0.12.3 * Added: April, 2020

igrec-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 08 Jun 2017 13:07:55 +0000

IgRepertoireConstructor IgRepertoireConstructor is a tool for construction of antibody repertoire and immunoproteogenomics analysis Information * Version: 3.0.0 * Added: June, 2017 * Link: Usage See which versions of igrec are available:

igsimulator-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 19 Mar 2020 10:33:10 +0000

IgSimulator IgSimulator is a versatile tool for simulation of immunoglobulin repertoire. Information * Version: git-c3778b74 * Added: March, 2020 * Link: Usage See which versions of igsimulator are available: $ module avail igsimulator

igv-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 26 Dec 2017 14:55:21 +0000

Integrative Genomics Viewer (IGV) Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. Information * Latest Version: 2.4.5 * Added: June, 2014 * Updated: February, 2017

igvtools-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 26 Dec 2017 15:05:05 +0000

Integrative Genomics Viewer (IGV) Tools Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. Information * Latest Version: 2.3.98 * Updated: December, 2017

infernal-software

anonymous@undisclosed.example.com (Anonymous) — Sat, 20 Jul 2019 12:57:23 +0000

Infernal Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their prim…

installing_gbrowse2

anonymous@undisclosed.example.com (Anonymous) — Tue, 14 Feb 2012 14:12:32 +0000

1. Install prerequisites sudo perl -MCPAN -e 'install Math::BigInt::Pari' sudo perl -MCPAN -e 'install Digest::SHA' sudo perl -MCPAN -e 'install Crypt::SSLeay' sudo perl -MCPAN -e 'install Net::OpenID::Consumer' sudo perl -MCPAN -e 'install Net::SMTP::SSL' sudo perl -MCPAN -e 'install Authen::SASL'

integron-finder-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 08 Nov 2023 11:48:55 +0000

integron-finder Bioinformatics tool to find integrons in bacterial genomes. Information * Version: 2.0.2 * Added: November, 2023 * Link: Usage See which versions are available: $ module avail integron-finder Load one version into your environment and run it:

interproscan-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 28 May 2019 07:43:50 +0000

Interproscan InterPro is a database which integrates together predictive information about proteins' function from a number of partner resources, giving an overview of the families that a protein belongs to and the domains and sites it contains. Information

interproscan

anonymous@undisclosed.example.com (Anonymous) — Thu, 21 Jul 2011 10:27:33 +0000

Interproscan Official FTP: Installation Requirements From the readme, in addition to Bioperl, these packages must be installed on the head node and any compute nodes! Make sure they work! 1.1 Perl The InterProScan package has been developed in Perl5 under UNIX and requires that various perl modules be installed beforehand. Please note that all these modules are available via the CPAN website (http://search.cpan.org/) * DB_File.pm - the in…

ip_numbers

anonymous@undisclosed.example.com (Anonymous) — Sat, 22 May 2010 14:19:32 +0000

IP numbers hpc.ilri.cgiar.org - 192.168.5.3, 41.204.190.10 BecA-Net webserver - 192.168.5.4, 41.204.190.11 ILRI proxy - 172.26.0.166:80 LDAP - 172.26.0.218 ilri.cgiarad.org LIMS - 172.26.0.101 CIP-HPC - 216.244.151.133 ICRISAT-HPC - 220.227.242.214

iqtree-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 15 May 2025 05:48:27 +0000

iqtree Efficient software for phylogenomic inference. Information * Version: 2.4.0 * Added: August, 2020 * Updated: May, 2025 * Link: Usage See versions which are available: $ module avail iqtree Load one version into your environment and run it:

ivar-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 05 Sep 2021 09:25:56 +0000

ivar iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. Information * Version: 1.3.1 * Added: January, 2021 * Updated: September, 2021 * Link: Usage See versions of ivar that are available:

java_jar_files

anonymous@undisclosed.example.com (Anonymous) — Sat, 22 May 2010 14:19:32 +0000

Using JAR Files: The Basics Extracting the Contents a JAR File The basic command to use for extracting the contents of a JAR file is: jar xf jar-file [archived-file(s)] Creating a JAR File The basic format of the command for creating a JAR file is:

jclusterfunk-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 21 May 2025 10:59:04 +0000

jclusterfunk A command line tool with a bunch of functions for trees. Information * Latest version: 0.0.25 * Added: May, 2025 * Link: Usage See which versions are available: $ module avail jclusterfunk Load one version into your environment and run it:

jellyfish-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 28 Oct 2020 09:20:18 +0000

Jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. Information * Latest version: 2.3.0 * Added: March, 2015 * Updated: October, 2020 * Link: Usage See versions of jellyfish which are available: $ module avail jellyfish

juicebox-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 11 Nov 2020 11:37:09 +0000

Juicebox tools Visualization and analysis software for Hi-C data Information * Version: 1.11.08 * Added: November, 2020 * Link: Usage See versions of juicebox which are available: $ module avail juicebox Load one version into your environment and run it:

juicer-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 19 Jan 2021 07:54:41 +0000

Juicer Juicer is a platform for analyzing kilobase resolution Hi-C data. In this distribution, we include the pipeline for generating Hi-C maps from fastq raw data files and command line tools for feature annotation on the Hi-C maps. Information *

kaiju-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 09 Nov 2021 08:23:22 +0000

Kaiju Kaiju is a program for the taxonomic classification of high-throughput sequencing reads, e.g., Illumina or Roche/454, from whole-genome sequencing of metagenomic DNA. Information * Latest Version: 1.8.2 * Added: November, 2016 * Updated: November, 2021

kallisto-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 22 Sep 2016 12:19:12 +0000

Kallisto kallisto is a program for quantifying abundances of transcripts from RNA-Seq data. Information * Latest Version: 0.43.0 * Added: March, 2016 * Updated: September, 2016 * Link: Usage See which versions of kallisto are available:

kaptive-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 20 Aug 2025 09:34:10 +0000

Kaptive Kaptive reports information about surface polysaccharide loci for Klebsiella pneumoniae species complex and Acinetobacter baumannii genome assemblies. Information * Version: 3.1.0 * Added: July, 2025 * Link: Usage See which versions are available:

karect-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 14 Feb 2019 23:33:51 +0000

karect KAUST Assembly Read Error Correction Tool. Information * Version: 1.0 * Added: February, 2019 * Link: Usage See versions of karect which are available: $ module avail karect Load one version into your environment and run it: $ module load karect/1.0 $ karect

kat-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 27 Sep 2017 11:52:02 +0000

KAT KAT is a suite of tools that generate, analyse and compare k-mer spectra produced from sequence files. Information * Version: 2.3.4 * Added: September, 2017 * Link: Usage See versions of kat which are available: $ module avail kat Load one version into your environment and run it:

kernel_compiling

anonymous@undisclosed.example.com (Anonymous) — Thu, 07 Apr 2011 08:12:14 +0000

Kernel compiling Kernels shipped with Linux distributions are, for stability reasons, old. Security fixes from current "stable" kernels are backported into the distro kernels. This means that if the stock kernel with your Linux distribution is working fine with the machine's hardware and workload then you should stick to the distro's kernel (as it will receive automated, hassle-free updates from the distro's repositories).

kleborate-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 25 Aug 2025 09:25:51 +0000

kleborate Kleborate was primarily developed to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC). Information * Version: 3.2.4 * Added: August, 2025 * Link: Usage See which versions are available:

kma-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 04 Mar 2025 07:01:29 +0000

kma KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend. KMA is particulary good at aligning high quality reads against highly redundant databases, where unique matches often does not exist. It works for long low quality reads as well, such as those from Nanopore. Non-unique matches are resolved using the "ConClave" sorting scheme, and a consensus sequence are outputtet in addition to other common attributes, base…

kmc-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 06 May 2025 09:42:30 +0000

KMC KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files. Information * Version: 3.1.1 * Added: November, 2018 * Updated: May, 2025 * Link: Usage See versions of kmc which are available: $ module avail kmc

kmer-ssr-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 16 Nov 2017 15:28:25 +0000

kmer-ssr Fast, Accurate, and Complete SSR Detection in Genomic Sequences. Information * Version: git-4043c0e7 * Added: November, 2017 * Link: Usage See which versions of kmer-ssr are available: $ module avail kmer-ssr Load kmer-ssr in your environment and run it:

kmerfreq-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 10 Jul 2023 08:23:54 +0000

kmerfreq kmerfreq count K-mer (with size K) frequency from the input sequence data, typically sequencing reads data, and reference genome data is also applicable. The forward and reverse strand of a k-mer are taken as the same k-mer, and only the kmer strand with smaller bit-value is used to represent the kmer. It adopts a 16-bit integer with max value 65535 to store the frequency value of a unique K-mer, and any K-mer with frequency larger than 65535 will be recorded as 65535. The program stor…

kmergenie-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 24 May 2017 06:57:31 +0000

KmerGenie KmerGenie estimates the best k-mer length for genome de novo assembly. Information * Version: 1.7044 * Added: February, 2017 * Updated: May, 2017 * Link: Usage See which versions of kmergenie are available: $ module avail kmergenie

kraken-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 11 Aug 2023 10:13:08 +0000

kraken A taxonomic sequence classifier that assigns taxonomic labels to short DNA reads. Information * Version: 2.1.2 * Added: August, 2016 * Updated: July, 2022 * Link: Usage See which versions are available: $ module avail kraken Load one version into your environment and run it:

krona-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 14 Feb 2023 15:05:59 +0000

krona Interactively explore metagenomes and more from a web browser. Information * Version: 2.8.1 * Added: March, 2022 * Link: Usage See which versions are available: $ module avail krona Load one version into your environment and run it:

last-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 16 Jun 2020 12:52:32 +0000

LAST LAST finds similar regions between sequences, and aligns them. It is designed for comparing large datasets to each other. Information * Version: 1066 * Added: June, 2020 * Link: Usage See versions of last that are available: $ module avail last

libsvm-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 16 Jul 2015 07:06:51 +0000

LibSVM LibSVM - A Library for Support Vector Machines. Information * Latest Version: 3.20 * Added: June, 2014 * Updated: July, 2015 * Link: Usage See versions of libsvm which are available: $ module avail libsvm Installation Notes from the sysadmin during installation:

lighter-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 14 Feb 2019 23:35:21 +0000

lighter Lighter is a kmer-based error correction method for whole genome sequencing data. Information * Version: 1.1.2 * Added: February, 2019 * Link: Usage See versions of lighter which are available: $ module avail lighter Load one version into your environment and run it:

list-of-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 09 Apr 2026 08:52:41 +0000

List of Software In general you can use the command module avail to show you the list of available software and their versions. Sometimes there are other software packages installed which aren't listed via the modules system; if you're curious you can look around in

longshot-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 20 Feb 2023 12:16:30 +0000

longshot Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). It takes as input an aligned BAM/CRAM file and outputs a phased VCF file with variants and haplotype information. It can also genotype and phase input VCF files. It can output haplotype-separated BAM files that can be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs), but it can genot…

lordec-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 17 Nov 2019 09:38:35 +0000

lordec LoRDEC processes data coming from high throughput sequencing machines of the second and third generations. These data are called sequencing reads, or simply reads for short. Technically speaking it processes short reads and long reads to correct errors in the long reads.

ltr_retriever-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 18 Feb 2022 14:06:03 +0000

LTR_retriever LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package. Information * Version: 2.9.0 * Added: February, 2022 * Link: Usage

mafft-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 07 Sep 2023 09:39:01 +0000

mafft MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.

make-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 24 Mar 2016 13:46:41 +0000

GNU Make GNU Make is a tool which controls the generation of executables and other non-source files of a program from the program's source files. Information * Version: 4.1 * Added: March, 2016 * Link: Usage See which versions of make are available:

maker-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 01 Nov 2021 09:11:24 +0000

Maker MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. Information * Version: 3.01.03

mapsplice-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 24 Mar 2016 13:49:01 +0000

MapSplice MapSplice is a software for mapping RNA-seq data to reference genome for splice junction discovery that depends only on reference genome. Information * Version: 2.2.0 * Added: March, 2016 * Link: Usage See which versions of mapsplice are available:

marginalign-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 04 Nov 2018 16:45:55 +0000

marginAlign The marginAlign package can be used to align reads to a reference genome and call single nucleotide variations (SNVs). It is specifically tailored for Oxford Nanopore Reads. Information * Version: git-git-2369dafd * Added: November, 2018

marginpolish-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 26 Sep 2019 11:49:18 +0000

MarginPolish MarginPolish is a graph-based assembly polisher. It iteratively finds multiple probable alignment paths for run-length-encoded reads and uses these to generate a refined sequence. It takes as input a FASTA assembly and an indexed BAM (ONT reads aligned to the assembly), and it produces a polished FASTA assembly.

mash-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 04 May 2020 18:38:09 +0000

mash Fast genome and metagenome distance estimation using MinHash. * Latest Version: 2.2 * Added: January, 2018 * Updated: May, 2020 * Link: Usage Show all available versions of mash: $ module avail mash Load a particular version of mash and run it:

masurca-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 26 Jun 2023 09:07:44 +0000

MaSuRCA The MaSuRCA (Maryland Super Read Cabog Assembler) assembler combines the benefits of deBruijn graph and Overlap-Layout-Consensus assembly approaches. Since version 3.2.1 it supports hybrid assembly with short Illumina reads and long high error PacBio/MinION data.

maxbin2-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 15 Mar 2020 10:42:09 +0000

MaxBin2 MaxBin2 is the next-generation of MaxBin that supports multiple samples at the same time. MaxBin is a software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Users could understand the underlying bins (genomes) of the microbes in their metagenomes by simply providing assembled metagenomic sequences and the reads coverage information or sequencing reads.

mcl-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 17 Jul 2018 08:40:40 +0000

mcl The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs. Information * Latest version: 14-137 * Added: July, 2018

mcscanx-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 17 Feb 2023 13:44:52 +0000

MCScanX Multiple Collinearity Scan toolkit X version. Information * Version: mcscanx/git-97e74f40 * Added: September, 2021 * Link: Usage See which versions of mcscanx are available: $ module avail mcscanx Load one version into your environment and run it:

mecat-software

anonymous@undisclosed.example.com (Anonymous) — Sat, 10 Nov 2018 16:12:09 +0000

MECAT An ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads. Information * Version: git-d04bfa84 (developer does not tag proper release versions) * Added: November, 2018 * Link: Usage See versions of MECAT which are available:

medaka-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 13 May 2025 12:27:57 +0000

medaka medaka is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods operating on basecalled data, and can be competitive with state-of-the-art signal-based methods, whilst being much faster.

megahit-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 06 May 2025 10:07:00 +0000

MEGAHIT single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. Information * Version: 1.2.9 * Added: July, 2017 * Updated: February, 2022

megax-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 30 Jun 2019 20:42:26 +0000

Mega X Sophisticated and user-friendly software suite for analyzing DNA and protein sequence data from species and populations. Information * Version: 10.0.5 * Added: June, 2019 * Link: Usage See versions of megax which are available: $ module avail megax

merqury-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 02 Aug 2024 19:10:42 +0000

Merqury Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality reference.

meryl-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 01 Aug 2024 19:52:43 +0000

Meryl This is 'meryl', a near total rewrite of 'meryl' that appeared in both project kmer and Celera Assembler. Information * Version: 1.4.1 * Added: August, 2024 * Link: Usage See which versions are available: $ module avail meryl Load one version into your environment and run it:

metabat-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 25 Sep 2017 10:23:56 +0000

MetaBAT MetaBAT is an efficient tool for accurately reconstructing single genomes from complex microbial communities. Information * Version: 2.12.1 * Added: September, 2017 * Link: Usage See versions of metabat which are available: $ module avail megahit

metaeuk-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 09 Jan 2022 14:12:23 +0000

metaeuk MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs. MetaEuk combines the fast and sensitive homology search capabilities of MMseqs2 with a dynamic programming procedure to recover optimal exons sets. It reduces redundancies in multiple discoveries of the same gene and resolves conflicting gene predictions on the same strand.

metaphlan-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 19 Jul 2023 08:36:13 +0000

metaphlan MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.

metis-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 25 Oct 2019 12:27:51 +0000

Metis METIS - Serial Graph Partitioning and Fill-reducing Matrix Ordering. Information * Version: 5.1.0 * Added: January, 2017 * Link: Usage See which versions of metis are available: $ module avail metis Load one version into your environment:

migec-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 22 Aug 2016 07:44:05 +0000

MIGEC Molecular Identifier Guided Error Correction pipeline that provides several useful tools for analysis of immune repertoire sequencing data. Information * Version: 1.2.4a * Added: August, 2016 * Link: Usage See which versions of migec are available:

migmap-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 08 Mar 2017 13:08:10 +0000

MiGMAP MiGMAP is a mapper for full-length T- and B-cell repertoire sequencing. Information * Latest version: 1.0.2 * Added: March, 2017 * Link: Usage See versions of migmap which are available: $ module avail migmap Load migmap: $ module load migmap

miniasm-software

anonymous@undisclosed.example.com (Anonymous) — Sat, 10 Nov 2018 15:47:44 +0000

miniasm Ultrafast de novo assembly for long noisy reads (though having no consensus step). Information * Latest version: 0.3 * Added: November, 2018 * Link: Usage See versions of miniasm that are available: $ module avail miniasm Load one version into your environment and run it:

minimac3-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 25 Jul 2022 15:52:35 +0000

minimac3 Minimac3 is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac and minimac2. Information * Version: 2.0.1 * Added: July, 2022 * Link: Usage See which versions are available:

minimac4-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 17 Jun 2022 07:16:56 +0000

minimac4 Minimac4 is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac/mininac2/minimac3. Information * Version: 1.0.3 * Added: June, 2022 * Link: Usage See which versions are available:

minimap2-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 03 Mar 2025 07:23:16 +0000

minimap2 A versatile pairwise aligner for genomic and spliced nucleotide sequences. Information * Latest version: 2.28 * Added: November, 2018 * Updated: March, 2025 * Link: Usage See versions that are available: $ module avail minimap2

minpath-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 24 Jul 2017 07:52:05 +0000

MinPath MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset. Information

mira-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 23 Mar 2015 20:25:10 +0000

Mira MIRA - Sequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data. * Version: 4.0.2 * Added: December, 2014 * Link: Usage * Show all available versions of mira module avail mira * Load mira module:

mirdeep2-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 27 Apr 2020 14:24:56 +0000

mirdeep2 miRDeep2 discovers active known or novel miRNAs from deep sequencing data (Solexa/Illumina, 454, ...). Information * Latest version: 0.1.3 * Added: April, 2020 * Link: Usage See versions of mirdeep2 which are available: $ module avail mirdeep2

mitools-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 08 Mar 2017 12:55:25 +0000

MiTools MiTools is a Next Generation Sequencing (NGS) data processing tool (based on MiLib). Information * Latest version: 1.4 * Added: March, 2017 * Link: Usage See versions of MiTools which are available: $ module avail mitools Load mitools:

mixcr-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 04 Nov 2019 07:39:08 +0000

MiXCR MiXCR is a universal software for fast and accurate analysis of raw T- or B- cell receptor repertoire sequencing data. Information * Latest Version: 3.0.11 * Added: November, 2016 * Updated: November, 2019 * Link: Usage See which versions of mixcr are available:

mkatari-bioinformatcs-august-2013-screennotes

anonymous@undisclosed.example.com (Anonymous) — Mon, 09 Jun 2014 14:13:52 +0000

Back to Manny's Bioinformatics Workshop Home Some useful information about Screen Screen is a feature that allows you to reconnect to the terminal and continue where you have left off in an event of a power outage or network connection being lost. It is also useful in managing multiple instances.

mkatari-bioinformatics-august-2013-bioinformatics-august-2013-mpileup

anonymous@undisclosed.example.com (Anonymous) — Wed, 18 Nov 2015 19:48:39 +0000

Back to Manny's Bioinformatics Workshop Home Identifying SNPs using mpileup A quick way to call SNPs is to use mpileup which is one of the tools provided by samtools. However if you want control over your results, consider the GATK pipeline found Processing files and Running GATK|here. The steps to process the file are almost the same compared to the GATK pipeline, however mpileup allows you to provide the different groups (Read Groups) as separate bam files as well.Below is a recommended pipe…

mkatari-bioinformatics-august-2013-blastnotes

anonymous@undisclosed.example.com (Anonymous) — Thu, 04 Jun 2015 12:38:34 +0000

Back to Manny's Bioinformatics Workshop Home This page contains a short introduction on how to create a Blast database and also how to run Blast using a query. Please replace your sequences with the names provided for the scripts to work for you. Please remember --- if you are planning to run Blast on command line, please do it in

mkatari-bioinformatics-august-2013-bowtienotes

anonymous@undisclosed.example.com (Anonymous) — Thu, 03 Jul 2014 13:19:27 +0000

Back to Manny's Bioinformatics Workshop Home Creating a Bowtie Index and Performing an alignment using Cassava as a reference This is a quick example of how to build a bowtie index and executing bowtie. Normally you will create the index only once you there is no need to create a special script for it. Just make sure you are in

mkatari-bioinformatics-august-2013-cleansnp

anonymous@undisclosed.example.com (Anonymous) — Mon, 19 Aug 2013 14:33:07 +0000

Back to Manny's Bioinformatics Workshop HOME Clean SNP file Read the file making sure explicitly tell it to delimit using tab and header is true Remember to save the file as a tab delimited text file. read.table("Draft sent to Manny.txt", sep="\t", header=T, row.names=1)->draft To count na use is.na. The number of True can be counted.

mkatari-bioinformatics-august-2013-clustering

anonymous@undisclosed.example.com (Anonymous) — Wed, 17 Jun 2015 13:26:50 +0000

Back to Manny's Bioinformatics Workshop HOME Clustering rna-seq data continuation from DESeq resSig.txt normalized.txt In case you didn't get DESeq to work download and load the files above resSig = read.table("resSig.txt", header=T) normalized = read.table("normalized.txt", header=T, row.names=1) Get the significant genes

mkatari-bioinformatics-august-2013-convert-snp

anonymous@undisclosed.example.com (Anonymous) — Mon, 19 Aug 2013 14:35:14 +0000

Back to Manny's Bioinformatics Workshop Home Converting SNP Format This is not the most efficient way to process this, however intuitively its the simplest. Initialize vectors to save output which can be combined later snpcol=character() gencol=character() allelesa=character() allelesb=character() confcol=character()

mkatari-bioinformatics-august-2013-deseq

anonymous@undisclosed.example.com (Anonymous) — Fri, 21 Aug 2015 14:13:39 +0000

Back to Manny's Bioinformatics Workshop HOME Here we will discuss how to create an R script (DESeq.R) that can be executed on HPC. This script has been adapted from the DESeq manual DESeq manual except paths to the files are replaced with variables and the plots are being saved as pdf documents in an output directory.

mkatari-bioinformatics-august-2013-gatknotes

anonymous@undisclosed.example.com (Anonymous) — Wed, 17 Aug 2016 08:37:25 +0000

Back to Manny's Bioinformatics Workshop Home Processing files and Running GATK GATK is a very powerful Variant calling software developed at Broad gatk that is recommended by many researchers. However there are some strict rules that it follows thus resulting in a pipeline that needs several steps. The steps below have been provided by notes from the link above.

mkatari-bioinformatics-august-2013-igvnotes

anonymous@undisclosed.example.com (Anonymous) — Wed, 21 May 2014 13:45:18 +0000

Back to Manny's Bioinformatics Workshop Home Processing Sam output for IGV To see sam file in igv NOTE !! The index file MUST be in the same directory as the file. 1) load samtools module module load samtools 2) Create an index for the genome fasta file samtools faidx Mesculenta_147.fa

mkatari-bioinformatics-august-2013-introlinuxnotes

anonymous@undisclosed.example.com (Anonymous) — Thu, 11 Jun 2015 11:50:24 +0000

Back to Manny's Bioinformatics Workshop Home What is Linux ? It is a free and open source operating system released in 1991 under the GNU GPL license.GPL allows anyone to use, modify and redistribute with the requirement that they pass it on with the same license. It is the leading operating system of choice for servers such as supercomputers. More than 90% of the top 500 fastest computers are based on Linux.

mkatari-bioinformatics-august-2013-loadingphytozome

anonymous@undisclosed.example.com (Anonymous) — Thu, 18 Jun 2015 09:05:26 +0000

Back to Manny's Bioinformatics Workshop Home Loading Phytozome Annotations Read Phytozome annotation file. This step was tricky because there were characters such as quotes and hash marks. We need to reset the default values to allow the file to load without a problem. Download the Arabidopsis annotation file here

mkatari-bioinformatics-august-2013-more-slurm

anonymous@undisclosed.example.com (Anonymous) — Mon, 09 Jun 2014 08:19:14 +0000

Back to Manny's Bioinformatics Workshop Home Some more useful SLURM notes Reading Variable from command line Building on Alan's notes on Using SLURM we can also provide an option to input the variables on the command line. Basically if you have ten different files you want to execute separately, you don't want to have to create 10 different files. One script should be able to do the job, but you simply must provide the input to the script.

mkatari-bioinformatics-august-2013-phytozome2gostats

anonymous@undisclosed.example.com (Anonymous) — Mon, 15 Aug 2016 09:47:39 +0000

Back to Manny's Bioinformatics Workshop HOME Phytozome is an excellent source of annotation and predicted go-term for genes of your plant species. Unfortunately not all of the species have an annotation database set to be used for GOStats. The functions below provide a simple way to create your own Gene Set Enrichment object which can be used in GoStats.

mkatari-bioinformatics-august-2013-vcfregion

anonymous@undisclosed.example.com (Anonymous) — Thu, 21 May 2015 13:43:50 +0000

Back to Manny's Bioinformatics Workshop Home Selecting a specific region in a vcf file In order to obtain a subset of the vcf file based on genome region please use the following command. Original documentation here module load tabix bgzip Genotypes2015.annotated.vcf tabix -p vcf /home/mkatari/Genotypes2015.annotated.vcf.gz tabix -p vcf /home/mkatari/Genotypes2015.annotated.vcf.gz Chromosome11:5532312-5532957

mkatari-bioinformatics-august-2013-volcano-plot

anonymous@undisclosed.example.com (Anonymous) — Fri, 16 Aug 2013 18:13:42 +0000

Back to Manny's Bioinformatics Workshop Home Volcano Plot using sample Microarray Data In this exercise we will practice our R-coding skills by analyzing a sample microarray dataset to create a Volcano plot. A volcano plot is a great visual aid to identify genes that are differentially expressed. The Log Fold Change is plotted on the x-axis and the -1 * Log base 10 of the p-value from a statistical test is plotted on the y-axis. Significantly differentially expressed genes have a p-value less …

mkatari-bioinformatics-august-2013

anonymous@undisclosed.example.com (Anonymous) — Wed, 25 Jan 2017 05:13:03 +0000

Manny's Bioinformatics Workshop Manny's workshop: * Introduction to Linux * Recommended software * Windows machines: MobaXterm * Apple machines: Xquartz * Linux notes * ppt * Alan's information about the Cluster Using the cluster * Alan's information about how to use SLURM

mlst-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 03 Mar 2025 08:51:58 +0000

mlst Scan contig files against PubMLST typing schemes. Information * Version: 2.23.0 * Added: February, 2025 * Link: Usage See which versions are available: $ module avail mlst Load one version into your environment and run it: $ module load mlst/2.23.0 $ mlst

mmseqs2-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 13 May 2025 09:02:55 +0000

MMseqs2 MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is free and open source software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile search…

modeller-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 21 Oct 2016 19:06:08 +0000

Modeller Modeller is a program for comparative protein structure modelling by satisfaction of spatial restraints. Information * Version: 9.17 * Added: October, 2016 * Link: Usage See which versions of modeller are available: $ module avail modeller

modeltest-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 15 May 2024 09:53:40 +0000

modeltest ModelTest-NG is a tool for selecting the best-fit model of evolution for DNA and protein alignments. ModelTest-NG supersedes jModelTest and ProtTest in one single tool, with graphical and command console interfaces. Information * Version: 0.1.7

monitoring

anonymous@undisclosed.example.com (Anonymous) — Thu, 29 Mar 2012 12:56:08 +0000

Nagios

mosdepth-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 15 Sep 2020 12:55:57 +0000

mosdepth fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing. Information * Version: 0.2.9 * Added: September, 2020 * Link: Usage See which versions of mosdepth are available: $ module avail mosdepth Load one version into your environment and run it:

mothur-krona-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 16 Aug 2016 06:50:43 +0000

mothur_krona A script to convert mothur taxonomy summary files to Krona XML format. Information * Version: git-87499a0 * Added: August, 2016 * Link: Usage See which versions of mothur_krona are available: $ module avail mothur_krona Load mothur_krona

mothur-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 01 Jul 2020 12:43:43 +0000

mothur mothur offers the ability to go from raw sequences to the generation of visualization tools to describe α and β diversity. Information * Latest version: 1.44.1 * Added: October, 2011 * Updated: July, 2020 * Link: Usage See versions of mothur which are available:

mrbayes-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 11 Sep 2023 07:17:20 +0000

mrbayes MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters. Information

multiqc-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 25 Apr 2022 14:29:01 +0000

MultiQC MultiQC is a reporting tool that parses summary statistics from results and log files generated by other bioinformatics tools. MultiQC doesn't run other tools for you - it's designed to be placed at the end of analysis pipelines or to be run manually when you've finished running your tools.

mummer-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 11 Nov 2020 11:26:17 +0000

MUMmer MUMmer is a versatile alignment tool for DNA and protein sequences. Information * Latest version: 4.0.0rc1 * Added: October, 2010 * Updated: November, 2020 * Link: Usage See versions which are available: $ module avail mummer Load one version into your environment and run it:

muscle-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 23 Feb 2023 06:10:52 +0000

MUSCLE MUSCLE is a multiple alignment program with accuracy and speed that are consistently better than CLUSTALW. Information * Version: 3.8.1551 * Added: April, 2020 * Updated: February, 2023 * Link: Usage See versions of muscle which are available:

nagios

anonymous@undisclosed.example.com (Anonymous) — Thu, 19 Jul 2012 06:56:21 +0000

Setup (On Debian Squeeze) Setup Check_by_ssh How to setup check_megaraid_sas Enable Nagios commands via web-interface

nanoplot-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 29 Apr 2025 08:18:24 +0000

nanoplot Plotting tool for long read sequencing data and alignments. Information * Version: 1.42.0 * Added: April, 2025 * Link: Usage See versions that are available: $ module avail nanoplot Load one version into your environment and run it:

nanopolish-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 22 Feb 2023 13:36:55 +0000

nanopolish Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more (see Nanopolish modules, below).

nanoq-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 29 Apr 2025 09:19:04 +0000

nanoq Ultra-fast quality control and summary reports for nanopore reads Information * Version: 0.10.0 * Added: April, 2025 * Link: Usage See versions that are available: $ module avail nanoq Load one version into your environment and run it:

nanoqc-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 06 Dec 2023 18:25:40 +0000

nanoqc Quality control tools for long read sequencing data aiming to replicate some of the plots made by fastQC. Information * Version: git-a7bcbdce * Added: December, 2023 * Link: Usage See versions that are available: $ module avail nanoqc

netmhcpan-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 10 Sep 2015 14:35:30 +0000

netmhcpan NetMHCpan uses Artificial Neural Networks(ANN) to predict peptides bindings to MHC molecules. Information * Latest Version: 2.8 * Added: September, 2015 * Link: Usage See versions of netmhcpan which are available: $ module avail netmhcpan

new_hardware

anonymous@undisclosed.example.com (Anonymous) — Sat, 22 May 2010 14:19:32 +0000

Hardware information At least half of the compute nodes are missing parts. List the parts needed here: Status Comments compute-0-1 Down Needs to be reinstalled

news

anonymous@undisclosed.example.com (Anonymous) — Tue, 02 May 2023 12:47:50 +0000

ILRI Research Computing News Here we will post news and announcements about the ILRI research-computing infrastructure, including important updates, breaking changes, etc. ---------- May 2, 2023: planned maintenance ILRI ICT is planning some major maintenance on our Nairobi infrastructure during the upcoming weekend.

nextalign-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 01 Apr 2022 08:02:33 +0000

nextalign Nextalign is a viral genome sequence alignment algorithm used in Nextclade, ported to C++ and made into the standalone command-line tool. Nextalign performs pairwise alignment of provided sequences against a given reference sequence using banded local alignment algorithm with affine gap-cost. Band width and rough relative positions are determined through seed matching.

nextclade-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 23 Feb 2023 12:11:44 +0000

nextclade Clade assignment, mutation calling, and sequence quality checks. This is the command line version of nextclade. Information * Version: 2.11.0 * Added: February, 2021 * Updated: February, 2023 * Link: Usage See versions which are available:

nextclip-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 26 Oct 2017 07:57:36 +0000

NextClip Nextera Long Mate Pair analysis and processing tool. Information * Version: 1.3.1 * Added: October, 2017 * Link: Usage See versions of nextclip which are available: $ module avail nextclip Load one version into your environment and run it:

nextflow-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 24 Jul 2025 19:15:21 +0000

nextflow Nextflow is a bioinformatics workflow manager that enables the development of portable and reproducible workflows. It supports deploying workflows on a variety of execution platforms including local, HPC schedulers, AWS Batch, Google Genomics Pipelines, and Kubernetes. Additionally, it provides support for manage your workflow dependencies through built-in support for Conda, Docker, Singularity, and Modules.

ngmlr-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 02 Sep 2020 09:51:28 +0000

ngmlr NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations. Information * Version: 0.2.7 * Added: September, 2020 * Link:

ngs-tools-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 21 Mar 2022 07:07:12 +0000

ngs-tools Information * Version: 3.0.0 * Added: March, 2022 * Link: Usage See versions which are available: $ module avail ngs-tools Load one version into your environment and run it: $ module load ngs-tools/3.0.0 $ sra-search $ compute-coverage

ngsqctoolkit-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 26 Aug 2014 07:47:54 +0000

====== NGS QC Toolkit ======A toolkit for the quality control (QC) of next generation sequencing (NGS) data. The toolkit comprises of user-friendly stand alone tools for quality control of the sequence data generated using Illumina and Roche 454 platforms with detailed results in the form of tables and graphs, and filtering of high-quality sequence data. It also includes few other tools, which are helpful in NGS data quality control and analysis.

nquire-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 10 May 2021 11:45:27 +0000

nQuire A statistical framework for ploidy estimation using NGS short-read data. Information * Version: git-a990a88e * Added: May, 2021 * Link: Usage See which versions of nQuire are available: $ module avail nQuire Load one version into your environment and run it:

ntcard-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 14 Feb 2017 06:55:28 +0000

ntCard ntCard is a streaming algorithm for cardinality estimation in genomics datasets. Information * Version: 1.0.0 * Added: February, 2017 * Link: Usage See which versions of ntcard are available: $ module avail ntcard Load ntcard $ module load ntcard/1.0.0

oases-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 27 May 2014 10:25:11 +0000

Oases De novo transcriptome assembler for very short reads. Information * Version: 0.2.08 * Added: May 27, 2014 * Link: When used in conjunction with one another, Velvet and Oases must be appropriately matched by version/release, and also, based upon the value of

ocaml-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 02 Dec 2014 06:35:55 +0000

Ocaml Ocaml is a popular variant of Caml language. it extends the core Caml language with a fully-fledged object-oriented layer, as well as a powerful module system, all connected by a sound, polymorphic type system featuring type inference v4.02.1

old_start

anonymous@undisclosed.example.com (Anonymous) — Thu, 25 Apr 2013 11:35:48 +0000

This is the old start page. As of April 25, 2013 it has been moved here to make room for newer, cleaner content and hierarchical structure ILRI Research Computing This is the ILRI Research Computing wiki. Here you'll find information about all aspects of the research computing infrastructure, including tutorials and usage information for users. Please use this wiki to document all changes you make to servers, services, and applications.

oligoarrayaux-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 13 Feb 2023 13:43:50 +0000

oligoarrayaux OligoArrayAux is a subset of the UNAFold package for use with OligoArray. Information * Version: 3,8,1 * Added: February, 2023 * Link: Usage See which versions are available: $ module avail oligoarrayaux Load one version into your environment:

opam-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 02 Dec 2014 06:49:00 +0000

Opam OPAM is a source-based package manager for OCaml. It supports multiple simultaneous compiler installations, flexible package constraints, and a Git-friendly development workflow. v1.2.0 * Version: 1.2.0 * Added: November, 2014 * Link:

openmpi

anonymous@undisclosed.example.com (Anonymous) — Sun, 23 Jan 2011 10:30:40 +0000

MPI OpenMPI is one implementation of the Message Passing Interface protocol, there is also MPICH2. There are various applications which benefit by being parallelized: * mpiBLAST * clustalw-mpi See the homepage for more information:

orp-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 31 Oct 2019 08:45:33 +0000

Oyster River Protocol Information * Version: 2.2.8 * Added: October, 2019 * Link: Usage See versions of orp that are available: $ module avail orp Load a particular version into your environment and run it: $ module load orp/2.2.8 $ /export/apps/orp/2.2.8/oyster.mk

pagan-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 22 Nov 2016 18:06:10 +0000

Pagan Pagan is a general-purpose tool for the alignment of sequence graphs. Information * Latest Version: 0.61 * Added: November, 2016 * Link: Usage See which versions of pagan are available: $ module avail pagan Load pagan $ module load pagan/0.61

pairfq-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 08 Oct 2015 12:49:50 +0000

pairfq Sync paired-end FASTA/Q files and keep singleton reads. Information * Version: 0.14.4 * Added: October, 2015 * Link: Usage See versions of pairfq which are available: $ module avail pairfq Load and run pairfq: $ module load pairfq/0.14.4 $ pairfq

paml-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 23 May 2016 08:06:32 +0000

PAML PAML(Phylogenetic Analysis by Maximum Likelihood) is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Information * Version: 4.9a * Added: November, 2012 * Updated: May, 2016 * Link:

panaroo-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 09 Aug 2023 07:01:04 +0000

panaroo A Bacterial Pangenome Analysis Pipeline. Shares information between genomes to correct errors. Can call large structural variants. Fast and scalable to over 10k bacterial genomes. Information * Version: 1.3.3 * Added: August, 2023 * Link:

pandaseq-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 08 Dec 2014 09:27:37 +0000

Pandaseq Pandaseq is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. Pandaseq 2.7 Information * Version: 2.7 * Added: October, 2014 * Link: Usage Show available version

pasta-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 21 Oct 2018 13:01:53 +0000

Pasta Practical Alignment using SATe and Transitivity. Information * Latest version: git-d939adb2 * Added: October, 2018 * Link: Usage See versions of Pasta that are available: $ module avail pasta Load one version into your environment and run it:

pathoscope-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 11 Mar 2022 08:25:12 +0000

pathoscope Species identification and strain attribution with unassembled sequencing data. Information * Version: 2.0.7 * Added: March, 2022 * Link: Usage See which versions are available: $ module avail pathoscope Load one version into your environment and run it:

pblat-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 10 May 2019 13:52:00 +0000

pblat When the query file format is fasta, you can specify many threads to process it. It can reduce run time linearly, and use almost equal memory as the original blat program. This is useful when you blat a big query file to a huge reference like human whole genome sequence.

pbsuite-software

anonymous@undisclosed.example.com (Anonymous) — Sat, 30 Sep 2017 06:35:36 +0000

PBSuite Software for Long-Read Sequencing Data from PacBio. Information * Version: 15.8.24 * Added: September, 2017 * Link: Usage See which versions of pbsuite are available: $ module avail pbsuite Load one version of pbsuite into your environment:

pear-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 16 Apr 2020 11:14:11 +0000

PEAR An ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. Information * Version: 0.9.6 * Added: September, 2016 * Updated: April, 2020 *

perl-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 14 May 2020 05:28:19 +0000

Perl Perl 5 is a highly capable, feature-rich programming language. Information * Version: 5.28.2 * Updated: May, 2020 * Link: Usage See which versions of perl are available: $ module avail perl Load one version into your environment and run it:

perl

anonymous@undisclosed.example.com (Anonymous) — Sat, 22 May 2010 14:19:32 +0000

Perl tips Installing mod_perl Quick start: Administration Enter the perl CPAN shell: * perl -MCPAN -e shell List installed module versions: * perl -MCPAN -e 'CPAN::Shell->r' List installed module versions (from inside the shell): *

pgdspider-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 17 Feb 2017 15:49:57 +0000

PGDSpider PGDSpider is a powerful automated data conversion tool for population genetic and genomics programs. Information * Version: 2.1.1.0 * Added: February, 2017 * Link: Usage See which versions of PGDSpider are available: $ module avail pgdspider

phylip-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 24 Aug 2017 06:15:42 +0000

Phylip PHYLIP is a free package of programs for inferring phylogenies. Information * Version: 3.696 * Added: August, 2017 * Link: Usage See versions of phylip which are available: $ module avail phylip Load one version into your environment:

phyml-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 16 Sep 2018 06:56:38 +0000

PhyML Phylogenetic estimation using Maximum Likelihood. Information * Version: 3.3.20180621 * Added: September, 2018 * Link: Usage See versions of phyml which are available: $ module avail phyml Load one version into your environment and run it:

picard-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 21 Nov 2022 08:01:57 +0000

Picard tools A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats. Information * Version: 2.27.5 * Added: March, 2015 * Updated: November, 2022 * Link: Usage See versions which are available:

picrust-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 08 Jan 2015 17:33:28 +0000

PICRUSt PICRUSt is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. v1.0.0 * Version: 1.0.0 * Added: January, 2015 * Link: Usage * Show all available versions of picrust

pilon-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 06 May 2025 07:38:34 +0000

pilon Pilon is a software tool which can be used to automatically improve draft assemblies find variation among strains, including large event detection. Information * Version: 1.24 * Added: November, 2018 * Updated: May, 2025 * Link: Usage

plasmidid-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 26 Jun 2023 14:45:21 +0000

plasmidid PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification. Information * Version: 1.6.5 * Added: September, 2020 * Updated: June, 2023 * Link:

platanus-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 14 Nov 2014 12:45:33 +0000

Platanus * Platanus is a de novo assembler designed to assemble high-throughput data. It can handle highly heterozygotic samples. * First, it constructs contigs using the algorithm based on de Bruijn graph. * Second, the order of contigs is determined according to paired-end (mate-pair) data and constructs scaffolds.

plink-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 09 Dec 2019 09:10:41 +0000

PLINK PLINK is a whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. Information * Version: 2.00-alpha (Nov 28, 2019) * Added: October, 2011 * Updated: December, 2019

pod5-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 06 Dec 2023 08:49:30 +0000

pod5 POD5 is a file format for storing nanopore dna data in an easily accessible way. The format is able to be written in a streaming manner which allows a sequencing instrument to directly write the format. Data in POD5 is stored using Apache Arrow, allowing users to consume data in many languages using standard tools.

polyphen-software

anonymous@undisclosed.example.com (Anonymous) — Sat, 01 Apr 2017 15:56:48 +0000

PolyPhen-2 PolyPhen-2 (Polymorphism Phenotyping v2) is a software tool which predicts possible impact of amino acid substitutions on the structure and function of human proteins using straightforward physical and evolutionary comparative considerations.

polypolish-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 13 May 2025 12:46:53 +0000

polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other polishers, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. Polypolish is also a conservative polisher, so it is very unlikely to introduce new errors during polishing.

poplddecay-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 24 Jan 2022 18:49:29 +0000

poplddecay PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Information * Version: 3.41 * Added: January, 2022 * Link: Usage See which versions of poplddecay are available:

porechop-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 13 May 2025 13:04:53 +0000

porechop Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity.

pplacer-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 12 Mar 2020 14:57:42 +0000

pplacer Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.

prank-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 19 Jan 2018 15:32:52 +0000

PRANK PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. Information * Version: 170427 * Added: April, 2016 * Updated: January, 2018 * Link: Usage See which versions of prank are available: $ module avail prank

presto-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 15 Mar 2020 11:54:48 +0000

pRESTO pRESTO is a toolkit for processing raw reads from high-throughput sequencing of lymphocyte repertoires. Information * Version: 0.5.13 * Added: June, 2016 * Updated: March, 2020 * Link: Usage See which versions of presto are available:

primalscheme-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 18 May 2022 13:45:57 +0000

primalscheme A tool for designing primer panels for multiplex PCR. Information * Version: 1.3.2 * Added: May, 2022 * Link: Usage See versions which are available: $ module avail primalscheme Load one version into your environment and run it:

prinseq-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 21 Apr 2020 07:45:18 +0000

prinseq PRINSEQ can be used to filter, reformat, or trim your genomic and metagenomic sequence data. It generates summary statistics of your sequences in graphical and tabular format. It is easily configurable and provides a user-friendly interface.

prodigal-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 13 Feb 2023 12:29:31 +0000

prodigal Fast, reliable protein-coding gene prediction for prokaryotic genomes. Information * Version: 2.6.3 * Added: March, 2020 * Link: Usage See which versions of prodigal are available: $ module avail prodigal Load one version into your environment and run it:

prokka-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 07 May 2025 12:42:22 +0000

Prokka Prokka is a software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. Information * Version: 1.14.6 * Added: February, 2017 * Updated: May, 2020 * Link: Usage See which versions are available:

provean-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 28 Mar 2018 12:01:07 +0000

provean PROVEAN (Protein Variation Effect Analyzer) is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein. Information * Latest version: 1.1.5 * Added: March, 2018 *

pspp

anonymous@undisclosed.example.com (Anonymous) — Sat, 22 May 2010 14:19:32 +0000

PSPP - A Protein Structure Prediction Pipeline for Computing Clusters Protein structures are critical for understanding the mechanisms of biological systems and, subsequently, for drug and vaccine design. Unfortunately, protein sequence data exceed structural data by a factor of more than 200 to 1. This gap can be partially filled by using computational protein structure prediction. While structure prediction Web servers are a notable option, they often restrict the number of sequence queries a…

purge-haplotigs-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 20 Jun 2021 08:59:58 +0000

purge_haplotigs A simple pipeline for reassigning primary contigs that should be labelled as haplotigs. Information * Version: 1.1.1 * Added: June, 2021 * Link: Usage See which versions of purge_haplotigs are available: $ module avail purge_haplotigs

python-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 28 Feb 2025 14:01:00 +0000

python Python programming language. Standalone python for use with environment modules that need something other than the system's Python. Information * Version: 3.10 (3.10.16) * Added: October, 2014 * Updated: February, 2025 * Link: Usage

qiime-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 26 Mar 2017 16:06:24 +0000

QIIME QIIME™ (canonically pronounced chime) stands for Quantitative Insights Into Microbial Ecology. QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. Information * Version: 1.9.1

qiime2-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 05 Oct 2021 15:34:56 +0000

QIIME2 QIIME™ (canonically pronounced chime) stands for Quantitative Insights Into Microbial Ecology. QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. QIIME2 is a completely new and different version than QIIME1.

quast-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 07 Apr 2020 08:27:46 +0000

quast QUAST (QUality ASsessment Tool) evaluates genome assemblies by computing various metrics. Information * Latest Version: 5.0.2 * Added: September, 2014 * Updated: April, 2020 * Link: Usage See versions of quast which are available:

quickmerge-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 01 Oct 2019 15:07:37 +0000

quickmerge A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies. Information * Latest Version: 0.3 * Added: September, 2019 * Link: Usage See versions of quickmerge which are available: $ module avail quickmerge

quorum-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 06 Mar 2017 13:33:27 +0000

Quorum Quorum (Quality Optimized Reads from the University of Maryland) is an error corrector for Illumina reads. Information * Latest version: 1.1.1 * Added: March, 2017 * Link: Usage See versions of Quorum which are available: $ module avail quorum

r-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 12 Mar 2026 06:38:17 +0000

R R is a free software environment for statistical computing and graphics. Information * Version: 4.5 (4.5.2) * Added: February, 2015 * Updated: March, 2026 * Link: Usage See which versions are available: $ module avail R Load one version into your environment and run it:

racon-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 14 May 2025 09:02:24 +0000

racon Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Te…

raid

anonymous@undisclosed.example.com (Anonymous) — Sun, 19 Sep 2010 23:58:24 +0000

RAID We have two RAIDs on the HPC * Linux kernel software RAID * 3ware hardware RAID Drive numbering If you're looking at the front of the HPC you'll see four rows of drives. From the bottom: * Rows 0 - 2 are SATA, connected to the hardware 3ware RAID card

randfold-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 27 Apr 2020 13:35:03 +0000

Randfold Information * Latest version: 2.0.1 * Added: April, 2020 * Link: Usage See versions of randfold which are available: $ module avail randfold Load one version into your environment and run it: $ module load randfold/2.0.1 $ randfold

rapidnj-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 12 May 2025 05:55:18 +0000

rapidnj RapidNJ is an algorithmic engineered implementation of canonical neighbour-joining. It uses an efficient search heuristic to speed-up the core computations of the neighbour-joining method that enables RapidNJ to outperform other state-of-the-art neighbour-joining implementations. The RapidNJ method was originally presented in:

rapsearch-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 03 May 2020 14:13:13 +0000

rapsearch RAPSearch stands for Reduced Alphabet based Protein similarity Search. Information * Version: 2.22 * Added: May, 2020 * Link: Usage See versions of rapsearch which are available: $ module avail rapsearch Load one version into your environment and run it:

rasusa-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 29 Apr 2025 09:48:06 +0000

rasusa Randomly subsample sequencing reads or alignments. Information * Version: 2.1.0 * Added: April, 2025 * Link: Usage See versions that are available: $ module avail rasusa Load one version into your environment and run it: $ module load rasusa/2.1.0 $ rasusa

ratt-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 01 Feb 2017 12:27:56 +0000

RATT RATT(Rapid Annotation Transfer Tool) is a software to transfer annotation from a reference (annotated) genome to an un-annotated query genome. Information * Latest Version: r18 * Added: February, 2017 * Link: Usage See versions of RATT which are available:

raven-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 13 May 2025 13:17:47 +0000

raven Raven is a de novo genome assembler for long uncorrected reads. Information * Version: 1.8.3 * Added: May, 2025 * Link: Usage See versions which are available: $ module avail raven Load one version into your environment and run it:

raxml-ng-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 12 May 2025 06:15:49 +0000

raxml-ng RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. RAxML-NG is a successor of RAxML (Stamatakis 2014) and leverages the highly optimized likelihood computation implemented in libpll (Flouri et al. 2014).

raxml-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 14 May 2025 12:03:10 +0000

RAxML RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. Information * Latest Version: 8.2.12 * Added: June, 2011 * Updated: May, 2025 *

ray-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 09 Jun 2015 16:37:22 +0000

Ray Ray is a parallel software that computes de novo genome assemblies with next-generation sequencing data. Ray is written in C++ and can run in parallel on numerous interconnected computers using the message-passing interface (MPI) standard. Information

rcorrector-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 24 Jan 2023 14:12:38 +0000

rcorrector Rcorrector(RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. Rcorrector can also be applied to other type of sequencing data where the read coverage is non-uniform, such as single-cell sequencing. Information

rdp-classifier-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 15 Sep 2015 09:37:56 +0000

RDP Classifier RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. Information * Version: 2.11 * Added: September, 2015

recon-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 17 Mar 2021 12:44:49 +0000

recon De Novo Repeat Finder. Patched and updated by the RepeatMasker team. Information * Version: 1.0.8 * Added: March, 2021 * Link: Usage See versions of recon which are available: $ module avail recon Load one version into your environment and run it:

repeatmasker-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 14 Dec 2021 09:17:44 +0000

RepeatMasker RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Currently over 56% of human genomic sequence is identified and masked by the program.

repeatmodeler-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 17 Mar 2021 16:46:59 +0000

RepeatModeler RepeatModeler is a de novo transposable element (TE) family identification and modeling package. At the heart of RepeatModeler are three de-novo repeat finding programs ( RECON, RepeatScout and LtrHarvest/Ltr_retriever ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data.

repeatscout-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 17 Mar 2021 12:53:43 +0000

RepeatScout RepeatScout - De Novo Repeat Finder. Information * Version: 1.0.6 * Added: March, 2021 * Link: Usage See versions of repeatscout which are available: $ module avail repeatscout Load one version into your environment and run it:

repseqio-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 19 Mar 2020 09:48:26 +0000

repseqio Utils for manipulations with RepSeq data. Information * Version: 1.3.3 * Added: March, 2020 * Link: Usage See which versions of repseqio are available: $ module avail repseqio Load one version into your environment and run it:

resfinder-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 16 May 2025 14:52:36 +0000

resfinder ResFinder identifies acquired genes and/or finds chromosomal / mutations mediating antimicrobial resistance in total or / partial DNA sequence of bacteria. Information * Version: 4.7.2 * Added: March, 2025 * Updated: May, 2025 * Link:

rgi-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 14 Feb 2023 11:27:35 +0000

rgi Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models. Information * Version: 6.0.2 * Added: February, 2023 * Link: Usage See which versions are available:

rmblast-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 16 Mar 2021 13:18:19 +0000

rmblast RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program "rmblastn" for use with RepeatMasker and RepeatModeler.

roary-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 24 Nov 2023 08:31:01 +0000

roary Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka) and calculates the pan genome. Information * Version: 3.13.0 * Added: October, 2023 * Link: Usage See which versions are available:

rocks_commands

anonymous@undisclosed.example.com (Anonymous) — Sat, 22 May 2010 14:19:32 +0000

Rocks commands Rocks 5.0 includes a command line tool rocks to handle most system administration tasks. Boot-related commands Reinstall a node Nodes' BIOS should be set to boot from PXE (network) first and then the local hard drives. The PXE server changes the PXE configs depending on what

root-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 16 May 2017 18:09:24 +0000

root A modular scientific software framework. It provides all the functionalities needed to deal with big data processing, statistical analysis, visualisation and storage. It is mainly written in C++ but integrated with other languages such as Python and R.

rpm

anonymous@undisclosed.example.com (Anonymous) — Wed, 21 Mar 2012 12:14:00 +0000

Redhat Package Manager Tips Check if a package is installed: $ rpm -qa | grep core openoffice.org-core-2.3.0-6.10.el5 coreutils-5.97-19.el5 policycoreutils-1.33.12-14.2.el5 List files in a certain package: $ rpm -ql coreutils List files in an RPM:

rrnaselector-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 17 Dec 2015 13:09:44 +0000

rRNASelector rRNASelector selects rRNA genes from metagenomic and metatranscriptomic sequences. Information * Version: 1.1 * Added: December, 2015 * Link: Usage See versions of rRNASelector which are available: $ module avail rrnaselector

rsem-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 22 Jul 2025 18:50:14 +0000

RSEM RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. * Version: 1.3.3 * Added: February, 2015 * Updated: July, 2025 * Link: Usage Show all available versions: $ module avail RSEM Load one version into your environment:

rseqc-software

anonymous@undisclosed.example.com (Anonymous) — Sat, 11 Feb 2017 09:14:04 +0000

RSeQC RSeQC: An RNA-seq Quality Control Package. RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Information * Latest Version: 2.6.4 * Added: February, 2017

ruby-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 18 Dec 2023 08:48:32 +0000

Ruby Ruby is an open source programming language with a focus on simplicity and productivity. Information * Version: 3.1 (3.1.4) * Added: October, 2015 * Updated: December, 2023 * Link: Usage See which versions are available: $ module avail ruby

sailfish-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 24 Mar 2016 13:51:55 +0000

Sailfish Rapid Mapping-based Isoform Quantification from RNA-Seq Reads. Information * Version: 0.9.2 * Added: March, 2016 * Link: Usage See which versions of sailfish are available: $ module avail sailfish Load sailfish $ module load sailfish/0.9.2

salmon-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 09 Feb 2026 13:31:50 +0000

salmon Salmon is a tool for fast transcript quantification from RNA-seq data. It requires a set of target transcripts (either from a reference or de-novo assembly) to quantify. Information * Latest Version: 1.10.0 * Added: September, 2016 * Updated: February, 2026

salsa-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 24 Jan 2021 09:44:49 +0000

SALSA A tool to scaffold long read assemblies with Hi-C data. Information * Version: git-974589f3 * Added: November, 2020 * Link: Usage See which versions of salsa are available: $ module avail salsa Load one version into your environment and run it:

samba

anonymous@undisclosed.example.com (Anonymous) — Sat, 22 May 2010 14:19:32 +0000

Configuring Samba for Segolip Segolip's unit has many customers who use the HPC to analyze data from the labs. Segolip has several administrative users who are in charge of copying data to/from the HPC and into the proper customers' folders. These administrators have read/write access to the root of the Segolip data, under which they will move data to the appropriate places for their customers to access. Customers are not allowed to write in these folders, so they must use the data where it …

samclip-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 30 Apr 2025 10:02:32 +0000

samclip Filter SAM file for soft and hard clipped alignments. Information * Version: 0.4.0 * Added: April, 2025 * Link: Usage See which versions are available: $ module avail samclip Load one version into your environment and run it: $ module load samclip/0.4.0 $ samclip

samtools-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 05 Dec 2025 07:16:20 +0000

samtools samtools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. * Latest Version: 1.22.1 * Added: February, 2015 * Updated: December, 2025

satsuma2-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 29 Sep 2021 07:49:09 +0000

satsuma2 Information * Version: git-37c5f386 * Added: September, 2021 * Link: Usage See versions of satsuma2 that are available: $ module avail satsuma2 Load one version into your environment and run it: $ module load satsuma2/git-37c5f386 $ SatsumaSynteny2

scipio-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 17 Feb 2016 06:17:19 +0000

Scipio Scipio is a tool for identifying eukaryotic genes. Information * Version: 1.4.1 * Added: February, 2016 * Link: Usage See which versions of scipio are available: $ module avail scipio Load scipio $ module load scipio/1.4.1 Installation

scythe-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 24 Jun 2015 09:00:11 +0000

scythe Scythe uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. It considers quality information, which can make it robust in picking out 3'-end adapters, which often include poor quality bases. Information * Version: 0.994-beta

sepp-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 28 Dec 2021 13:49:08 +0000

sepp SEPP stands for "SATe-enabled Phylogenetic Placement", and addresses the problem of phylogenetic placement of short reads into reference alignments and trees. Information * Version: 4.5.1 * Added: May, 2020 * Updated: December, 2021 *

seqkit-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 25 Feb 2026 11:52:24 +0000

seqkit SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. Information * Version: 2.12.0 * Added: February, 2018 * Updated: February, 2026 * Link: Usage See which versions are available: $ module avail seqkit

seqqs-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 12 Mar 2015 10:40:29 +0000

seqqs Seqqs (SEQuence Quality Statistics, pronounced "seeks") is a C library for quickly gathering quality statistics from sequence files. Information * Version: git-3d053750 * Added: March, 2015 * Link: Usage See versions of seqqs which are available

seqtk-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 06 May 2025 09:46:35 +0000

seqtk Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Information * Version: 1.4 * Added: February, 2018 * Updated: May, 2025 * Link: Usage See which versions are available: $ module avail seqtk

seqwish-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 15 Sep 2020 13:25:09 +0000

seqwish seqwish implements a lossless conversion from pairwise alignments between sequences to a variation graph encoding the sequences and their alignments. As input we typically take all-versus-all alignments, but the exact structure of the alignment set may be defined in an application specific way. This algorithm uses a series of disk-backed sorts and passes over the alignment and sequence inputs to allow the graph to be constructed from very large inputs that are commonly encountered when …

seroba-software

anonymous@undisclosed.example.com (Anonymous) — Sat, 17 Nov 2018 20:57:42 +0000

seroba SeroBA is a k-mer based Pipeline to identify the Serotype from Illumina NGS reads for given references. You can use SeroBA to download references from PneumoCaT to do identify the capsular type of Streptococcus pneumoniae. Information * Version: 1.0.0

shannon_cpp-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 24 Jan 2023 14:09:57 +0000

shannon_cpp Shannon is a novel de novo RNA-Seq assembler designed based on information-theoretic principles. We develop its C++ implementation here, which significantly improves both time and memory efficiency by an order of magnitude than its original (currently deprecated) Python prototype.

shannon-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 03 Mar 2017 07:09:36 +0000

Shannon Shannon is a program for assembling transcripts from RNA-Seq data. Information * Version: 0.0.2 * Added: March, 2017 * Link: Usage See which versions of shannon are available: $ module avail shannon Load shannon $ module load shannon/0.0.2

shapeit-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 10 Jul 2023 06:26:14 +0000

shapeit SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data. Information * Version: 2.904 * Added: July, 2023 * Link: Usage See which versions are available: $ module avail shapeit

shasta-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 15 Mar 2020 11:19:08 +0000

shasta De novo assembly from Oxford Nanopore reads. Information * Version: 0.4.0 * Added: September, 2019 * Updated: March, 2020 * Link: Usage See versions of shasta which are available: $ module avail shasta Load one version into your environment and run it:

shovill-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 06 May 2025 10:03:16 +0000

shovill The SPAdes genome assembler has become the de facto standard de novo genome assembler for Illumina whole genome sequencing data of bacteria and other small microbes. SPAdes was a major improvement over previous assemblers like Velvet, but some of its components can be slow and it traditionally did not handle overlapping paired-end reads well.

sickle-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 25 Jul 2016 07:09:46 +0000

sickle sickle is a windowed adaptive trimming tool for FASTQ files using quality Information * Version: 1.33 * Added: July, 2016 * Link: Usage See which versions of sickle are available: $ module avail sickle Load sickle $ module load sickle/1.33

sidebar

anonymous@undisclosed.example.com (Anonymous) — Tue, 08 Mar 2022 06:24:33 +0000

Resources * Using the Cluster * Using SLURM * List of Software * Biological Databases * Trainings archive * FAQ Platform * About * Servers Contact * Alan Orth * Jean-Baka Domelevo Entfellner

sift-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 28 Feb 2017 12:36:42 +0000

SIFT SIFT predicts whether an amino acid substitution affects protein function. Information * Version: 4.0.3b * Added: February, 2017 * Link: Usage See which versions of sift are available: $ module avail sift Load sift/4.0.3b $ module load sift/4.0.3b

sistr-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 15 Jan 2018 17:15:04 +0000

sistr Serovar predictions from whole-genome sequence assemblies by determination of antigen gene and cgMLST gene alleles using BLAST. Mash MinHash can also be used for serovar prediction. * Latest Version: 1.0.2 * Added: January, 2018 * Link:

ska2-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 12 May 2025 06:37:21 +0000

ska2 Split k-mer analysis (version 2) uses exact matching of split k-mer sequences to align closely related sequences, typically small haploid genomes such as bacteria and viruses. SKA can only align SNPs further than the k-mer length apart, and does not use a gap penalty approach or give alignment scores. But the advantages are speed and flexibility, particularly the ability to run on a reference-free manner (i.e. including accessory genome variation) on both assemblies and reads. Citation

skesa-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 06 May 2025 08:41:56 +0000

SKESA SKESA is a de-novo sequence read assembler for microbial genomes. It uses conservative heuristics and is designed to create breaks at repeat regions in the genome. This leads to excellent sequence quality without significantly compromising contiguity. If desired, SKESA contigs could be connected into a GFA graph using GFA connector.

smalt-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 24 Mar 2016 13:53:55 +0000

Smalt SMALT aligns DNA sequencing reads with a reference genome. Information * Version: 0.7.6 * Added: March, 2016 * Link: Usage See which versions of smalt are available: $ module avail smalt Load smalt $ module load smalt/0.7.6 Installation

smartdenovo-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 10 Apr 2019 06:37:24 +0000

smartdenovo SMARTdenovo is a de novo assembler for PacBio and Oxford Nanopore (ONT) data. It produces an assembly from all-vs-all raw read alignments without an error correction stage. It also provides tools to generate accurate consensus sequences, though a platform dependent consensus polish tools (e.g. Quiver for PacBio or Nanopolish for ONT) are still required for higher accuracy.

snakemake-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 18 Feb 2022 08:28:07 +0000

Snakemake The Snakemake workflow management system is a tool to create reproducible and scalable data analyses Information * Version: 6.15 (real version 6.15.5) * Added: October, 2019 * Updated: February, 2022 * Link: Usage See versions of snakemake which are available:

sniffles-software

anonymous@undisclosed.example.com (Anonymous) — Sat, 22 Aug 2020 14:22:23 +0000

sniffles Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Please note the current version of Sniffles requires sorted output from BWA-MEM (use -M and -x parameter), Minimap2 (sam file with Cigar & MD string) or NGMLR.

snippy-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 30 Apr 2025 09:19:10 +0000

Snippy Rapid haploid variant calling and core genome alignment. Information * Version: 4.6.0 * Added: July, 2023 * Link: Usage See which versions are available: $ module avail snippy Load one version into your environment and run it: $ module load snippy/4.6.0 $ snippy

snp-dists-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 19 Nov 2025 12:29:15 +0000

snp-dists Pairwise SNP distance matrix from a FASTA sequence alignment. Information * Version: 0.8.2 * Added: November, 2025 * Link: Usage See versions which are available: $ module avail snp-dists Load one version into your environment and run it:

snp-pipeline-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 29 Jan 2019 13:53:01 +0000

SNP Pipeline The CFSAN SNP Pipeline is a Python-based system for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety. Information * Version: 1.0.1

snpeff-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 12 Jun 2023 17:49:01 +0000

SnpEff SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes). SnpSift is a toolbox that allows you to filter and manipulate annotated files. Information

snpmeta-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 23 May 2016 12:45:08 +0000

SNPMeta SNPMeta is a Python and BioPython-based tool to generate "metadata" for single nucleotide polymorphisms (SNPs) for easy filtering, or submission to SNP databases. Information * Version: 2.0 * Added: May, 2016 * Link: Usage See which versions of snpmeta are available:

soapaligner-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 24 Mar 2016 13:57:52 +0000

SOAPaligner/soap2 Genome-wide ab initio detection of splice junction sites from RNA-Seq. Information * Version: 2.21 * Added: March, 2016 * Link: Usage See which versions of SOAPaligner are available: $ module avail SOAPaligner Load SOAPaligner

soapdenovo-trans-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 11 Jan 2017 08:21:45 +0000

SOAPdenovo-Trans SOAPdenovo-Trans is a de novo transcriptome assembler inherited from the SOAPdenovo2 framework, designed for assembling transcriptome with alternative splicing and different expression level. Information * Version: 1.03 * Added: January, 2017

soapdenovo2-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 11 Apr 2018 14:22:36 +0000

SOAPdenovo2 SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. Information * Version: git-c4d2f5ee * Added: October, 2014 * Updated: April, 2018 * Link: Usage See versions of SOAPdenovo2 which are available:

soapsnp-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 26 Mar 2018 21:00:20 +0000

SOAPsnp SOAPsnp is a member of the SOAP (Short Oligonucleotide Analysis Package). Despite its name, the program is a resequencing utility that can assemble consensus sequence for the genome of a newly sequenced individual based on the alignment of the raw sequencing reads on the known reference.

soapsplice-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 24 Mar 2016 13:59:07 +0000

SOAPsplice Genome-wide ab initio detection of splice junction sites from RNA-Seq. Information * Version: 1.10 * Added: March, 2016 * Link: Usage See which versions of SOAPsplice are available: $ module avail SOAPsplice Load SOAPsplice $ module load SOAPsplice/1.10

solexaqa-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 10 Feb 2015 11:48:45 +0000

SolexaQA++ SolexaQA calculates sequence quality statistics and creates visual representations of data quality for second-generation sequencing data. v3.1.3 * Version: 3.1.3 * Added: February, 2015 * Link: Usage * Show all available versions of SolexaQA++

sourmash-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 29 Jan 2019 12:19:51 +0000

sourmash sourmash is a command-line tool and Python library for computing MinHash sketches from DNA sequences, comparing them to each other, and plotting the results. This allows you to estimate sequence similarity between even very large data sets quickly and accurately.

spades-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 30 May 2025 07:39:59 +0000

SPAdes SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. Information * Version: 4.2.0 * Added: September, 2014 * Updated: May, 2025 * Link: Usage See versions which are available:

speedseq-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 08 Jun 2017 05:46:28 +0000

SpeedSeq A flexible framework for rapid genome analysis and interpretation. Information * Version: 0.1.2 * Added: June, 2017 * Link: Usage See versions of speedseq which are available: $ module avail speedseq Load and run speedseq: $ module load speedseq/0.1.2 $ speedseq

squid-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 27 Apr 2020 13:10:38 +0000

SQUID A C library that is bundled with much of the above software. C function library for sequence analysis. Information * Latest version: 1.9g * Added: April, 2020 * Link: Usage See versions of squid which are available: $ module avail squid

squirrel-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 22 May 2025 12:22:52 +0000

squirrel Some QUIck Reconstruction to Resolve Evolutionary Links Information * Version: 1.1.2 * Added: May, 2025 * Link: Usage See which versions are available: $ module avail squirrel Load one version into your environment and run it:

sra-tools-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 21 Mar 2022 07:09:14 +0000

sra-tools NCBI SRA (Sequence Read Archive) tools. Information * Version: 3.0.0 * Added: March, 2022 * Link: Usage See versions which are available: $ module avail sra-tools Load one version into your environment and run it: $ module load sra-tools/3.0.0 $ sratools $ fastconv

sratoolkit-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 11 Dec 2019 11:46:51 +0000

SRA Toolkit A collection of tools and libraries for using data in the INSDC Sequence Read Archives. Information * Latest version: 2.10.0 * Added: August, 2014 * Updated: December, 2019 * Link: Usage See versions of SRAToolkit which are available:

srprism-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 18 Mar 2022 11:51:25 +0000

srprism Single Read Paired Read Indel Substitution Minimizer. Information * Version: 3.1.2 * Added: March, 2022 * Link: Usage See versions which are available: $ module avail srprism Load one version into your environment and run it: $ module load srprism/3.1.2 $ srprism

srst2-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 10 Aug 2023 07:43:40 +0000

srst2 This program is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes. Information * Version: git-73f885f5

sspace-longread-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 17 Nov 2016 07:05:41 +0000

SSPACE-longread SSPACE-longread is a stand-alone program for scaffolding pre-assembled contigs using long reads. Information * Latest Version: 1.1 * Added: November, 2016 * Link: Usage See which versions of sspace-longread are available:

sspace-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 09 Oct 2014 08:37:00 +0000

sspace Information * Version: 3.0 * Added: October, 2014 * Link: Usage See versions of sspace which are available module avail sspace Then you can run SSPACE_Standard_v3.0.pl. Installation Notes from the sysadmin during installation: tar xf SSPACE-STANDARD-3.0_linux-x86_64.tar.gz sudo mkdir /export/apps/sspace sudo mv SSPACE-STANDARD-3.0_linux-x86_64 /export/apps/sspace/3.0 sudo chown -R root:root /export…

stacks-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 16 Jan 2023 07:57:52 +0000

stacks Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. * Version: 2.62 * Added: February, 2015 * Updated: January, 2023 * Link: Usage Show all available versions:

star-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 02 Jun 2022 13:44:24 +0000

STAR STAR (Spliced Transcripts Alignment to a Reference) is an RNA-seq aligner. Information * Version: 2.7.10a * Added: March, 2016 * Updated: June, 2022 * Link: Usage See which versions are available: $ module avail star Load one version into your environment and run it:

staramr-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 03 Mar 2025 06:46:33 +0000

staramr Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases. Information * Version: 0.11.0 * Added: February, 2025 * Link: Usage See versions that are available: $ module avail staramr Load one version into your environment and run it:

start

anonymous@undisclosed.example.com (Anonymous) — Mon, 19 Jun 2023 10:08:36 +0000

ILRI Research Computing This is the ILRI Research Computing wiki. Here you'll find information about the research computing infrastructure, including information about software, help using SLURM, etc. Help * Using the cluster * Using the SLURM job scheduler * List of software * Biological databases * Live cluster status * HPC Users Group (archive) Contact E-mail questions, comments, and or corrections to the maintainers of this wiki:

stringtie-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 11 Jun 2018 15:52:09 +0000

stringtie StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. Information * Version: 1.3.4d * Added: July, 2014 * Updated: June, 2018 * Link: Usage See versions of stringtie which are available:

stringtie2-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 09 Nov 2023 09:25:23 +0000

stringtie2 Transcript assembly and quantification for RNA-Seq. A fork of the earlier tool of the same name by Johns Hopkins. Information * Version: 2.2.1 * Added: May, 2022 * Updated: November, 2023 * Link: Usage See versions which are available: $ module avail stringtie2 Load one version into your environment and run it:

structure-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 13 Jun 2022 08:37:39 +0000

Structure Structure is a free software package for using multi-locus genotype data to investigate population structure. Information * Latest version: 2.3.4 * Added: June, 2014 * Link: Usage See which versions are available: $ module avail structure

subread-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 23 Aug 2018 10:46:04 +0000

subread Subread package: high-performance read alignment, quantification and mutation discovery Information * Latest version: 1.6.2 * Added: August, 2018 * Link: Usage See versions of subread which are available: $ module avail subread

tablet-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 16 Jan 2018 14:06:28 +0000

Tablet Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments. Information * Version: 1.17.08.17 * Added: December, 2015 * Updated: January, 2018 * Link: Usage See versions of tablet which are available:

tape

anonymous@undisclosed.example.com (Anonymous) — Sat, 22 May 2010 14:19:32 +0000

Tape backup system Tape backup is Tape back_up software Storix System Backup Administrator: /home/villierse/software/storix To run: sbadmin

tassel-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 22 Oct 2024 12:53:23 +0000

tassel TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium. Information * Version: 5.2.94 * Added: November, 2021 * Updated: October, 2024 * Link: Usage See which versions are available:

taxpasta-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 10 Mar 2025 12:49:43 +0000

taxpasta The main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pa…

tech_recipes

anonymous@undisclosed.example.com (Anonymous) — Thu, 19 Jan 2012 06:01:15 +0000

Tomcat Installation

tmiseq-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 15 Aug 2016 12:21:43 +0000

TMISeq Scripts A collection of python scripts for TMISeq Information * Version: 2016-01-31 * Added: August, 2016 * Link: Usage See which versions of tmiseq are available: $ module avail tmiseq Load tmiseq $ module load tmiseq/2016-01-31

todo

anonymous@undisclosed.example.com (Anonymous) — Sun, 29 Sep 2019 19:42:17 +0000

TODO For comments and reorganizing/prioritizing by Jean-Baka. * 2019-07-31: Install Oyster River Protocol for Sandra Kamenya and Erick Owuor * 2019-07-29: Install HyPhy for Vivien Chebii * 2019-07-26: Install RNAmmer on HPC for John Juma

tophat-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 23 Jul 2015 09:38:57 +0000

TopHat TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

tracer-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 28 Aug 2014 07:18:31 +0000

Tracer Tracer is a program for analysing the trace files generated by Bayesian MCMC runs (that is, the continuous parameter values sampled from the chain). It can be used to analyse runs of BEAST, MrBayes, LAMARC and possibly other MCMC programs. Information

trainings

anonymous@undisclosed.example.com (Anonymous) — Mon, 19 Sep 2016 12:00:52 +0000

Training and Capacity Building Bioinformatics is a relatively new specialist area. We need to raise awareness of the field here in Africa and expose local scientists to its potential. The West has spent millions of dollars sequencing the genomes of humans, animals, plants and parasites and the resulting data are freely available on the Internet. This is a vast body of knowledge that local scientists can use to solve their specific problems or to answer research questions. All scientists in Afri…

transabyss-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 24 Jan 2023 08:33:21 +0000

transabyss De novo assembly of RNAseq data using ABySS. Information * Version: 2.0.1 * Added: January, 2023 * Link: Usage See which versions are available: $ module avail transabyss Load one version into your environment and run it: $ module load transabyss/2.0.1 $ transabyss

transdecoder-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 11 Feb 2015 11:39:34 +0000

TransDecoder * TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

transrate-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 13 Jan 2017 06:41:08 +0000

Transrate Transrate is a software for de-novo transcriptome assembly quality analysis. Information * Version: 1.0.3 * Added: January, 2017 * Link: Usage See which versions of Transrate are available: $ module avail transrate Load transrate

treetime-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 28 Feb 2025 12:50:04 +0000

treetime Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction. TreeTime provides routines for ancestral sequence reconstruction and inference of molecular-clock phylogenies, i.e., a tree where all branches are scaled such that the positions of terminal nodes correspond to their sampling times and internal nodes are placed at the most likely time of divergence.

trf-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 01 Nov 2020 13:43:03 +0000

Tandem Repeats Finder Tandem repeats finder: a program to analyze DNA sequences. Information * Version: 4.0.9 * Added: February, 2015 * Updated: November, 2020 * Link: Usage See versions of trf which are available: $ module avail trf

trimgalore-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 15 Dec 2021 07:50:47 +0000

trimgalore Trim Galore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data. Information * Latest version: 0.6.7 * Added: December, 2021 * Link: Usage

trimmomatic-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 05 Sep 2021 11:10:43 +0000

Trimmomatic Trimmomatic is a flexible read trimming tool for Illumina NGS data. Information * Version: 0.39 * Added: September, 2015 * Updated: September, 2021 * Link: Usage See versions of Trimmomatic which are available: $ module avail trimmomatic

trinity-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 28 Oct 2020 11:28:26 +0000

Trinity Trinity assembles transcript sequences from Illumina RNA-Seq data. Information * Latest Version: v2.11.0 * Added: March, 2015 * Updated: October, 2020 * Link: Usage See versions of trinity which are available: $ module avail trinity

trinotate-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 17 Jul 2015 09:11:08 +0000

Trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Information * Version: 2.0.2 * Added: June, 2015

tutorials

anonymous@undisclosed.example.com (Anonymous) — Wed, 02 Sep 2020 11:39:37 +0000

Tutorials Here we list tutorials (mostly in bioinformatics) to guide you in your data analyses. Some are using UNIX commandline tools that are installed on the HPC, some are using the fabulous R software, and some are to be ran on graphical interface software such as the nice

twinscan-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 17 Feb 2016 05:53:57 +0000

Twinscan Twinscan predicts genes in eukaryotic genomic sequences. Information * Version: 3.5 * Added: February, 2016 * Link: Usage See which versions of twinscan are available: $ module avail twinscan Load twinscan $ module load twinscan/3.5

umi-tools-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 22 Aug 2016 07:34:36 +0000

UMI-tools Tools for dealing with Unique Molecular Identifiers. Information * Version: 0.2.3 * Added: August, 2016 * Link: Usage See which versions of umi-tools are available: $ module avail umi-tools Load umi-tools $ module load umi-tools/0.2.3

unicycler-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 12 Jun 2023 13:17:32 +0000

Unicycler Unicycler is an assembly pipeline for bacterial genomes. Information * Version: 0.5.0 * Added: February, 2019 * Updated: June, 2023 * Link: Usage See versions which are available: $ module avail unicycler Load one version into your environment and run it:

usearch-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 23 Jul 2015 10:28:46 +0000

usearch USEARCH is a unique sequence analysis tool with thousands of users world-wide. USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST. Information * Version: v8.0.1623 * Added: November, 2014

using-slurm

anonymous@undisclosed.example.com (Anonymous) — Thu, 05 Feb 2026 08:31:56 +0000

Using SLURM SLURM is a resource manager and job scheduler for high-performance computing clusters. We use a job scheduler to ensure fair usage of the research-computing resources by all users, with hopes that no one user can monopolize the computing resources. Users who wish to use the cluster must "request" CPU time and possibly "queue" for resources.

using-the-cluster

anonymous@undisclosed.example.com (Anonymous) — Fri, 06 Jan 2023 06:14:18 +0000

Using the Cluster ILRI's high-performance computing cluster is currently composed of four dedicated "compute" machines and four "storage" machines: * hpc: main login node, "head" of the cluster * compute05, compute06: used for batch and interactive jobs like BLAST, structure, R, etc (compute05 and compute06 have the newest AMD EPYC CPUs)

vcfdo-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 06 May 2021 10:07:40 +0000

vcfdo tools for processing and annotating VCF files, with focus on Plasmodium spp. Information * Version: git-508cc19b * Added: May, 2021 * Link: Usage See versions of vcfdo which are available: $ module avail vcfdo Load one version into your environment and run it:

vcflib-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 19 Aug 2015 07:36:59 +0000

vcflib vcflib is a C++ library for parsing and manipulating VCF files. Information * Latest Version: git-7f1575e * Added: August, 2015 * Updated: August, 2015 * Link: Usage See versions of vcflib which are available: $ module avail vcflib

vcftools-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 15 Mar 2021 10:10:09 +0000

VCFtools VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. Information * Latest Version: 0.1.16 * Added: December, 2012 * Updated: March, 2021 * Link: Usage See which versions of VCFtools are available:

velvet-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 06 May 2025 08:52:22 +0000

Velvet Sequence assembler for very short reads. Information * Version: 1.2.10 * Added: November, 2012 * Updated: May, 2025 * Link: Usage See versions which are available: $ module avail velvet Load one version into your environment and run it:

velvetoptimiser-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 14 Mar 2022 14:34:31 +0000

VelvetOptimiser Automatically optimise three of Velvet's assembly parameters. Information * Version: 2.2.6 * Added: March, 2022 * Link: Usage See which versions are available: $ module avail velvetoptimiser Load one version into your environment and run it:

vep-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 22 May 2023 06:10:51 +0000

Variant Effect Predictor (VEP) VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Information * Latest Version: 109.3

vg-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 15 Sep 2020 19:03:52 +0000

vg tools for working with genome variation graphs. Information * Version: 1.27.0 * Added: September, 2020 * Link: Usage See which versions of vg are available: $ module avail vg Load changeo into your environment: $ module load vg/1.27.0

viennarna-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 27 Apr 2020 12:24:17 +0000

ViennaRNA The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. Information * Latest version: 2.4.14 * Added: April, 2020 * Link: Usage See versions of vienna which are available:

virusdetect-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 06 Jun 2018 20:10:05 +0000

VirusDetect VirusDetect is a software package that can efficiently and exhaustively analyze large-scale sRNA sequence datasets for known and novel virus identification. Information * Version: 1.7 * Added: June, 2018 * Link: Usage See versions of virusdetect which are available:

vntrseek-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 18 Mar 2016 11:09:49 +0000

VNTRseek VNTRseek is a computational pipeline for the detection of VNTRs. Information * Version: 1.08 * Added: March, 2016 * Link: Usage See which versions of vntrseek are available: $ module avail vntrseek Load vntrseek $ module load vntrseek/1.08

vsearch-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 14 May 2018 10:21:15 +0000

vsearch VSEARCH stands for vectorized search, as the tool takes advantage of parallelism in the form of SIMD vectorization as well as multiple threads to perform accurate alignments at high speed. VSEARCH uses an optimal global aligner (full dynamic programming Needleman-Wunsch), in contrast to USEARCH which by default uses a heuristic seed and extend aligner. This usually results in more accurate alignments and overall improved sensitivity (recall) with VSEARCH, especially for alignments with …

w2rap-contigger-software

anonymous@undisclosed.example.com (Anonymous) — Mon, 25 Sep 2017 13:18:35 +0000

w2rap-contigger An Illumina PE genome contig assembler, can handle large (17Gbp) complex (hexaploid) genomes. Information * Version: git-a43f5a05 * Added: September, 2017 * Link: Usage See versions of w2rap-contigger which are available:

w2rap-software

anonymous@undisclosed.example.com (Anonymous) — Sun, 29 Oct 2017 12:34:53 +0000

w2rap WGS (Wheat) Robust Assembly Pipeline. Information * Version: git-60781b6c * Added: October, 2017 * Link: Usage See versions of w2rap which are available: $ module avail w2rap Load one version into your environment: $ module load w2rap/git-60781b6c

wemboss

anonymous@undisclosed.example.com (Anonymous) — Sat, 22 May 2010 14:19:32 +0000

wEMBOSS Web GUI for Emboss bioinformatics tools: # wget http://downloads.sourceforge.net/project/wemboss/wEMBOSS/wEMBOSSDIST-2.1.1/wEMBOSSDIST-2.1.1.tar.gz?use_mirror=garr # tar zxf wEMBOSSDIST-2.1.1.tar.gz # cd wEMBOSSDIST-2.1.1/wEMBOSSinstall/

whatshap-software

anonymous@undisclosed.example.com (Anonymous) — Wed, 27 Jun 2018 10:39:57 +0000

WhatsHap WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads. Information * Version: 0.16

wise-software

anonymous@undisclosed.example.com (Anonymous) — Fri, 07 Nov 2014 17:20:50 +0000

wise Information * Version: 2.4.1 * Added: November, 2014 Usage See versions of wise which are available module avail wise Installation Notes from the sysadmin during installation: $ cd /tmp $ wget http://ftp-stud.hs-esslingen.de/ubuntu/pool/universe/w/wise/wise_2.4.1.orig.tar.gz $ tar xf wise_2.4.1.orig.tar.gz $ cd wise-2.4.1/src $ scl enable devtoolset-2 bash $ sed -i 's/getline/getline_new/' HMMer2/sqio.c $ sed -i '23 s/isnumber/isdigit/' models/phasemodel.c $ make all $ cd dyc $ …

wombat-software

anonymous@undisclosed.example.com (Anonymous) — Thu, 13 Feb 2020 17:49:19 +0000

WEOMBAT WOMBAT is a program to facilitate analyses fitting a linear, mixed model via restricted maximum likelihood (REML). Information * Version: 2020-02-07 * Added: February, 2020 * Link: Usage See versions of wombat which are available:

wtdbg2-software

anonymous@undisclosed.example.com (Anonymous) — Tue, 09 Jul 2019 14:43:43 +0000

wtdbg2 Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Information