ILRI Research Computing

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====== 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 ///export/apps// to see if you can find what you're looking for.

Otherwise, here is a feeble attempt to list the software we have installed at ILRI, their versions, and (possibly) anyone who has experience running it. We endeavor to keep this list updated as the One True List™.

^Name           ^Latest version                ^How to load                 ^Contact   ^
|abacas|1.3.1|''module load abacas/1.3.1''| |
|[[abricate-software|abricate]]|1.0.1|''module load abricate/1.0.1''| |
|[[abyss-software|abyss]]|2.1.4|''module load abyss/2.1.4''| |
|[[ace-software|ace]]|1.01|''module load ace/1.01''| |
|[[ACT-software|ACT]]|13.0.0|''module load act/13.0.0''| |
|[[admixture-software|admixture]]|1.3.0|''module load admixture/1.3.0''| |
|[[adapterremoval-software|AdapterRemoval]]|1.5.4|''module load AdapterRemoval/1.5.4''| |
|[[aegean-software|aegean]]|0.16.0|''module load aegean/0.16.0''| |
|[[aliview-software|aliview]]|1.17.1|''module load aliview/1.17.1''| |
|[[amber-software|amber suite]]|12|''module load amber/12''| |
|[[ampssembler-software|ampssembler]]|git-51f0081|''module load ampssembler/git-51f0081''| |
|amos|3.1.0|''module load amos/3.1.0''| |
|[[angsd-software|angsd]]|0.910|''module load angsd/0.910''| |
|[[annovar-software|annovar]]|2016-02-01|''module load annovar/2016-02-01''| |
|[[antismash-software|antismash]]|7.0.0|''module load antismash/7.0.0''| |
|[[any2fasta-software|any2fasta]]|0.4.2|''module load any2fasta/0.4.2''| |
|apt|1.14.3|''module load apt/1.14.3''| |
|[[arb-software|arb]]|6.0.3|''module load arb/6.0.3''| |
|[[artemis-software|artemis]]|16.0.0|''module load act/16.0.0''| |
|[[artic-software|artic]]|1.2.3|''module load artic/1.2.3''| |
|[[artic-tools-software|artic-tools]]|0.3.1|''module load artic-tools/0.3.1''| |
|[[aspera-cli-software|aspera-cli]]|4.15.0|''module load aspera-cli/4.15.0''| |
|[[augustus-software|augustus]]|3.3|''module load augustus/3.3''| |
|[[awscli-software|awscli]]|2.4.0|''module load awscli/2''| |
|[[bam-readcount-software|bam-readcount]]|0.8.0|''module load bam-readcount/0.8.0''| |
|[[bamtools-software|bamtools]]|2.5.1|''module load bamtools/2.5.1''| |
|[[barrnap-software|barrnap]]|0.9|''module load barrnap/0.9''| |
|bayescan|2.1|''module load bayescan/2.1''| |
|[[bbmap-software|bbmap]]|38.95|''module load bbmap/38.95''| |
|[[bcftools-software|bcftools]]|1.15.1|''module load bcftools/1.15.1''| |
|bcl2fastq|2.20.0.422|''bcl2fastq''| |
|[[beagle-software|beagle]]|3.1.2|''module load beagle/3.1.2''| |
|[[beast-software|beast]]|1.10.4|''module load beast/1.10.4''| |
|[[beast2-software|beast2]]|2.6.4|''module load beast2/2.6.4''| |
|[[bedops-software|bedops]]|2.4.29|''module load bedops/2.4.29''| |
|[[bedtools-software|bedtools]]|2.29.0|''module load bedtools/2.29.0''| |
|[[binpacker-software|binpacker]]|1.0|''module load binpacker/1.0''| |
|[[bioperl-software|bioperl]]|1.7.2|''module load bioperl/1.7.2''| |
|[[bitseq-software|bitseq]]|0.7.5|''module load bitseq/0.7.5''| |
|[[blasr-software|blasr]]|smrtanalysis-4.0.0|''module load blasr/smrtanalysis-4.0.0''| |
|[[blast-software|blast]]|2.14.1+|''module load blast/2.14.1+''| |
|[[blobtools-software|blobtools]]|0.9.19.3|''module load blobtools/0.9.19.3''| |
|[[blat-software|blat]]|37x1|''module load blat/37x1''| |
|[[bmtagger-software|bmtagger]]|0.3.102.4|''module load bmtagger/0.3.102.4''| |
|[[bowtie-software|bowtie1]]|1.2.3|''module load bowtie/1.2.3''| |
|[[bowtie2-software|bowtie2]]|2.5.0|''module load bowtie2/2.5.0''| |
|[[brig-software|brig]]|0.95|''module load brig/0.95''| |
|[[busco-software|BUSCO ]]|5.2.2|''module load BUSCO/5.2.2''| |
|[[bwa-software|bwa]]|0.7.17|''module load bwa/0.7.17''| |
|[[cafe-software|cafe]]|4.1|''module load cafe/4.1''| |
|cangs|1.1|''module load cangs/1.1''| |
|[[canu-software|canu]]|1.8|''module load canu/1.8''| |
|cap3|latest|''module load cap3/latest''| |
|[[ccmetagen-software|ccmetagen]]|1.4.0|''module load ccmetagen/1.4.0''| |
|[[cd-hit-software|cd-hit]]|4.8.1|''module load cd-hit/4.8.1''| |
|[[cegma-software|cegma]]|v2.5|''module load cegma/v2.5''| |
|[[cgmlst-dists-software|cgmlst-dists]]|0.4.0|''module load cgmlst-dists/0.4.0''| |
|celera-wgs|6.1|''module load celera-wgs/6.1''| |
|censor|4.2.28|''module load censor/4.2.28''| |
|[[centrifuge-software|centrifuge]]|1.0.4|''module load centrifuge/1.0.4''| |
|[[changeo-software|changeo]]|1.2.0|''module load changeo/1.2.0''| |
|[[checkm-software|checkm]]|1.1.2|''module load checkm/1.1.2''| |
|[[chewbbaca-software|chewbbaca]]|git-87102063|''module load chewbbaca/git-87102063''| |
|[[circos-software|circos]]|0.69-9|''module load circos/0.69-9''| |
|[[clonalframe-software|clonalframe]]|1.2|''module load clonalframe/1.2''| |
|[[clonalframeml-software|clonalframeml]]|1.0|''module load clonalframeml/1.0''| |
|clustalw|2.1|''module load clustalw/2.1''| |
|[[cnvnator-software|CNVnator]]|0.3.3|''module load CNVnator/0.3.3''| |
|consed|20.0|''module load consed/20.0''| |
|[[cooler-software|cooler]]|0.8.10|''module load cooler/0.8.10''| |
|[[coperead-software|COPEread]]|1.1.2|''module load coperead/1.1.2''| |
|[[corset-software|corset]]|1.06|''module load corset/1.06''| |
|cufflinks|2.2.1|''module load cufflinks/2.2.1''| |
|[[cutadapt-software|cutadapt]]|3.5|''module load cutadapt/3.5''| |
|[[czid-cli-software|czid-cli]]|3.0.2|''module load czid-cli/3.0.2''| |
|[[dextractor-software|dextractor]]|git-a7f50c52|''module load dextractor/git-a7f50c52''| |
|dendroscope|2.7.4|''module load dendroscope/2.7.4''| |
|[[diamond-software|diamond]]|2.0.14|''module load diamond/2.0.14''| |
|[[disty-software|disty]]|0.1.0|''module load disty/0.1.0''| |
|[[dorado-software|dorado]]|0.5.0|''module load dorado/0.5.0''| |
|[[drep-software|drep]]|2.5.4|''module load drep/2.5.4''| |
|[[ea-utils-software|ea-utils]]|1.04.807|''module load ea-utils/1.04.807''| |
|[[eagle-software|eagle]]|2.4.1|''module load eagle/2.4.1''| |
|[[edirect-software|edirect]]| 7.80 | ''module load edirect/7.80'' | |
|[[eggnog-mapper-software|eggnog-mapper]]| 2.1.9 | ''module load eggnog-mapper/2.1.9'' | |
|eigenstrat|3.0|''module load eigenstrat/3.0''| |
|[[emblmygff3-software|emblmygff3]]|2.1|''module load emblmygff3/2.1''| |
|[[emboss-software|emboss]]|6.6.0|''module load emboss/6.6.0''| |
|[[easer-software|easer]]|1.7.0|''module load easer/1.7.0''| |
|est2uni|latest|''module load est2uni/latest''| |
|[[exabayes-software|exabayes]]|1.4.1|''module load exabayes/1.4.1''| |
|[[express-software|express]]|1.5.1|''module load express/1.5.1''| |
|[[falco-software|falco]]|0.3.0|''module load falco/0.3.0''| |
|[[falcon-phase-software|falcon-phase]]|git-7c50154e|''module load falcon-phase/git-7c50154e''| |
|[[fastANI-software|fastANI]]|1.3|''module load fastANI/1.3''| |
|[[fastp-software|fastp]]|0.22.0|''module load fastp/0.22.0''| |
|[[fastPHASE-software|fastPHASE]]|1.4.8|''module load fastPHASE/1.4.8''| |
|[[fastqc-software|fastqc]]|0.11.9|''module load fastqc/0.11.9''| |
|[[faststructure-software|fastSTRUCTURE]]|1.0|''module load fastSTRUCTURE/1.0''| |
|[[fasttree-software|fasttree]]|2.1.11|''module load fasttree/2.1.11''| |
|[[fastx-toolkit-software|fastx_toolkit]]|0.0.13|''module load fastx_toolkit/0.0.13''| |
|[[figaro-software|figaro]]|git-337aa9|''module load figaro/git-337aa9''| |
|figtree|1.4.0|''module load figtree/1.4.0''| |
|[[flapjack-software|flapjack ]]|1.18.04.23-beta|''module load flapjack/1.18.04.23-beta''| |
|[[flash-software|flash ]]|1.2.11|''module load FLASH/1.2.11''| |
|[[flash2-software|flash2]]|git-64826f45|''module load flash2/git-64826f45''| |
|[[flexbar-software|flexbar]]|2.7.0|''module load flexbar/2.7.8''| |
|[[flux-capacitor-software|flux-capacitor]]|1.6.1|''module load flux-capacitor/1.6.1''| |
|[[flye-software|flye]]|2.9|''module load flye/2.9''| |
|frappe|1.1|''module load frappe/1.1''| |
|[[fraggenescan-software|FragGeneScan ]]|1.30|''module load fraggenescan/1.30''| |
|[[freebayes-software|freebayes]]|1.3.4|''module load freebayes/1.3.4''| |
|[[funannotate-software|funannotate]]|1.8.15|See software page| |
|[[gassflow-software|GassFlow ]]|1.0|''module load gassflow/1.0''| |
|[[gatk-software|gatk]]|4.4.0.0|''module load gatk/4.4.0.0''| |
|[[gapfiller-software|gapfiller]]|1.10|''module load gapfiller/1.10''| |
|[[geneid-software|geneid]]|1.4.4|''module load geneid/1.4.4''| |
|[[genometools-software|genometools]]|1.6.1|''module load genometools/1.6.1''| |
|[[genomeworks-software|genomeworks]]|git-baab5668|''module load genomeworks/git-baab5668''| |
|[[genscan-software|genscan]]|latest|''module load genscan/latest''| |
|[[gffread-software|gffread]]|0.9.6|''module load gffread/0.9.6''| |
|glimmer|3.02|''module load glimmer/3.02''| |
|glu|1.0b3-prerelease4|''module load glu/1.0b3-prerelease4''| |
|[[gmap-software|gmap]]|2015-12-31|''module load gmap/2015-12-31''| |
|[[graphlan-software|graphlan]]|1.1.3|''module load graphlan/1.1.3''| |
|[[graphmap-software|graphmap]]|0.5.2|''module load graphmap/0.5.2''| |
|[[grom-rd-software|grom-rd]]|1.0|''module load grom-rd/1.0''| |
|[[gromacs-software|gromacs]]|2018.2|''module load gromacs/2018.2''| |
|[[groovy-software|groovy]]|2.4.9|''module load groovy/2.4.9''| |
|[[gsea-software|GSEA]]|2.2.3|''module load gsea/2.2.3''| |
|[[gtdbtk-software|gtdbtk]]|1.1.1|''module load gtdbtk/1.1.1''| |
|[[guidance-software|guidance]]|2.02|''module load guidance/2.02''| |
|[[guppy-software|guppy]]|6.2.1|''module load guppy/6.2.1''| |
|[[halcyon-software|halcyon]]|0.1.1|''module load halcyon/0.1.1''| |
|[[hapflk-software|hapflk]]|1.4|''module load hapflk/1.4''| |
|hapmix|2.0|''module load hapmix/2.0''| |
|[[hawk-software|hawk]]|git-a177811d|''module load hawk/git-a177811d''| |
|[[hclust2-software|hclust2]]|1.0.0|''module load hclust2/1.0.0''| |
|[[hdf5-software|hdf5]]|1.8.19|''module load hdf5/1.8.19''| |
|[[hmmer-software|hmmer]]|3.3|''module load hmmer/3.3''| |
|[[hmmIBD-software|hmmIBD]]|2.0.4|''module load hmmIBD/2.0.4''| |
|[[hpg-variant-software|hpg-variant]]|1.0|''module load hpg-variant/1.0''| |
|[[hic_qc-software|hic_qc]]|git-1e132fb2|''module load hic_qc/git-1e132fb2''| |
|[[hifiasm-software|hifiasm]]|0.16.1|''module load hifiasm/0.16.1''| |
|[[hisat2-software|hisat2]]|2.1.0|''module load hisat2/2.1.0''| |
|[[htseq-software|htseq]]|0.9.1|''module load htseq/0.9.1''| |
|[[htslib-software|htslib]]|1.15.1|''module load htslib/1.15.1''| |
|[[hypo-software|hypo]]|1.0.3|''module load hypo/1.0.3''| |
|[[hyphy-software|hyphy]]|2.5.48|''module load hyphy/2.5.48''| |
|[[idba-software|idba]]|1.1.2|''module load idba/1.1.2''| |
|[[igblast-software|igblast]]|1.10.0|''module load igblast/1.10.0''| |
|[[igdiscover-software|igdiscover]]|0.12.3|''module load igdiscover/0.12.3''| |
|[[igrec-software|igrec]]|3.0.0|''module load igrec/3.0.0''| |
|[[igsimulator-software|igsimulator]]|git-c3778b74|''module load igsimulator/git-c3778b74''| |
|[[iqtree-software|iqtree]]|2.2.0|''module load iqtree/2.2.0''| |
|[[igv-software|igv]]|2.4.5|''module load igv/2.4.5''| |
|[[igvtools-software|igvtools]]|2.3.98|''module load igvtools/2.3.98''| |
|[[infernal-software|infernal]]|1.1.2|''module load infernal/1.1.2''| |
|[[integron-finder-software|integron-finder]]|2.0.2|''module load integron-finder/2.0.2''| |
|[[interproscan-software|interproscan]]|5.13|''module load interproscan/5.13''| |
|i-tasser|latest|''module load i-tasser/latest''| |
|[[ivar-software|ivar]]|1.3.1|''module load ivar/1.3.1''| |
|[[jellyfish-software|jellyfish]]|2.3.0|''module load jellyfish/2.3.0''| |
|jMHC|1.5.0929|''module load jMHC/1.5.0929''| |
|[[juicebox-software|juicebox]]|1.11.08|''module load juicebox/1.11.08''| |
|[[juicer-software|juicer]]|1.6|''module load juicer/1.6''| |
|[[kaiju-software|kaiju]]|1.8.2|''module load kaiju/1.8.2''| |
|[[kallisto-software|kallisto]]|0.43.0|''module load kallisto/0.43.0''| |
|[[karect-software|karect]]|1.0|''module load karect/1.0''| |
|[[kat-software|kat]]|2.3.4|''module load kat/2.3.4''| |
|[[kma-software|kma]]|1.4.11|''module load kma/1.4.11''| |
|[[kmc-software|kmc]]|3.1.1|''module load kmc/3.1.1''| |
|[[kmerfreq-software|kmerfreq]]|git-90fca00d|''module load kmerfreq/git-90fca00d''| |
|[[kmergenie-software|kmergenie]]|1.7038|''module load kmergenie/1.7038''| |
|[[kmer-ssr-software|kmer-ssr]]|git-4043c0e7|''module load kmer-ssr/git-4043c0e7''| |
|[[kraken-software|kraken]]|2.1.2|''module load kraken/2.1.2''| |
|[[krona-software|krona]]|2.8.1|''module load krona/2.8.1''| |
|lamp|2.5|''module load lamp/2.5''| |
|lava|0.1|''module load lava/0.1''| |
|ldhat|2.1|''module load ldhat/2.1''| |
|[[libsvm-software|libsvm]]|3.20|''module load libsvm/3.20''| |
|[[lighter-software|lighter]]|1.1.2|''module load lighter/1.1.2''| |
|[[longshot-software|longshot]]|0.4.5|''module load longshot/0.4.5''| |
|[[lordec-software|lordec]]|0.9|''module load lordec/0.9''| |
|[[ltr_retriever-software|ltr_retriever]]|2.9.0|''module load ltr_retriever/2.9.0''| |
|lucy|1.19p|''module load lucy/1.19p''| |
|[[mafft-software|mafft]]|7.505|''module load mafft/7.505''| |
|[[maker-software|maker]]|3.01.03|''module load maker/3.01.03''| |
|[[mapsplice-software|mapsplice]]|2.2.0|''module load mapsplice/2.2.0''| |
|[[marginalign-software|marginalign]]|git-2369dafd|''module load marginalign/git-2369dafd''| |
|[[marginpolish-software|marginpolish]]|1.0.0|''module load marginpolish/1.0.0''| |
|[[mash-software|mash]]|2.2|''module load mash/2.2''| |
|[[masurca-software|masurca]]|4.1.0|''module load masurca/4.1.0''| |
|mauve|2.3.1|''module load mauve/2.3.1''| |
|[[maxbin2-software|maxbin2]]|2.2.7|''module load maxbin2/2.2.7''| |
|maximus|0.2|''module load maximus/0.2''| |
|[[mcl-software|mcl]]|14-137|''module load mcl/14-137''| |
|[[mcscanx-software|mcscanx]]|git-97e74f40|''module load mcscanx/git-97e74f40''| |
|[[mecat-software|MECAT]]|git-d04bfa84|''module load MECAT/git-d04bfa84''| |
|[[medaka-software|medaka]]|1.4.3|''module load medaka/1.4.3''| |
|[[megahit-software|megahit]]|1.2.9|''module load megahit/1.2.9''| |
|megan|4.70.4|''module load megan/4.70.4''| |
|[[megax-software|megax]]|10.0.5|''module load megax/10.0.5''| |
|[[metabat-software|metabat]]|2.12.1|''module load metabat/2.12.1''| |
|[[metaeuk-software|metaeuk]]|git-9818d1a5|''module load metaeuk/git-9818d1a5''| |
|[[metaphlan-software|metaphlan]]|4.0.6|''module load metaphlan/4.0.6''| |
|[[metis-software|metis]]|5.1.0|''module load metis/5.1.0''| |
|[[migec-software|migec]]|1.2.4a|''module load migec/1.2.4a''| |
|[[migmap-software|migmap]]|1.0.2|''module load migmap/1.0.2''| |
|[[miniasm-software|miniasm]]|0.3|''module load miniasm/0.3''| |
|[[minimac3-software|minimac3]]|2.0.1|''module load minimac3/2.0.1''| |
|[[minimac4-software|minimac4]]|1.0.3|''module load minimac4/1.0.3''| |
|[[minimap2-software|minimap2]]|2.24|''module load minimap2/2.24''| |
|[[minpath-software|MinPath]]|1.0.2|''module load MinPath/1.2''| |
|[[mira-software#v4.0.2|mira]]|4.0.2|''module load mira/4.0.2''| |
|[[mirdeep2-software|mirdeep2]]|0.1.3|''module load mirdeep2/0.1.3''| |
|[[mitools-software|mitools]]|1.4|''module load mitools/1.4''| |
|[[mixcr-software|mixcr]]|3.0.11|''module load mixcr/3.0.11''| |
|mkatari-ilri|latest|''module load mkatari-ilri/latest''| |
|[[modeller-software|modeller]]|9.17|''module load modeller/9.17''| |
|[[mosdepth-software|mosdepth]]|0.2.9|''module load mosdepth/0.2.9''| |
|[[mothur-software|mothur]]|1.44.1|''module load mothur/1.44.1''| |
|[[mothur-krona-software|mothur-krona]]|git-87499a0|''module load mothur-krona/git-87499a0''| |
|mpiblast|1.6.0|''module load mpiblast/1.6.0''| |
|[[mrbayes-software|mrbayes]]|3.2.7a|''module load mrbayes/3.2.7a''| |
|[[multiqc-software|multiqc]]|1.12|''module load multiqc/1.12''| |
|[[muscle-software|muscle]]|3.8.1551|''module load muscle/3.8.1551''|  |
|[[mummer-software|mummer]]|4.0.0rc1|''module load mummer/4.0.0rc1''| |
|[[nanopolish-software|nanopolish]]|0.14.0|''module load nanopolish/0.14.0''| |
|[[nanoqc-software|nanoqc]]|git-a7bcbdce|''module load nanoqc/git-a7bcbdce''| |
|[[netmhcpan-software|netmhcpan]]|2.8|''module load netmhcpan/2.8''| |
|[[nextalign-software|nextalign]]|1.11.0|''module load nextalign/1.11.0''| |
|[[nextclade-software|nextclade]]|2.11.0|''module load nextclade/2.11.0''| |
|[[nextclip-software|nextclip]]|1.3.1|''module load nextclip/1.3.1''| |
|[[nextflow-software|nextflow]]|23.10 (23.10.0)|''module load nextflow/23.10''| |
|[[ngs-tools-software|ngs-tools]]|3.0.0|''module load ngs-tools/3.0.0''| |
|[[ntcard-software|ntCard]]|1.0.0|''module load ntCard/1.0.0''| |
|[[ngmlr-software|ngmlr]]|0.2.7|''module load ngmlr/0.2.7''| |
|[[ngsqctoolkit-software|ngsqctoolkit]]|2.3.3|''module load ngsqctoolkit/2.3.3''| |
|[[nQuire-software|nQuire]]|git-a990a88e|''module load nQuire/git-a990a88e''| |
|novacraft|3.02.07|''module load novacraft/3.02.07''| |
|[[oases-software|oases]]|0.2.08|''module load oases/0.2.08''| |
|[[ocaml-software#v4.02.1|ocaml]]|4.02.1|''module load ocaml/4.02.1''| |
|[[oligoarrayaux-software|oligoarrayaux]]|3.8.1|''module load oligoarrayaux/3.8.1''| |
|[[opam-software#v1.2.0|opam]]|1.2.0|''module load opam/1.2.0''| |
|orthomcl|2.0.3|''module load orthomcl/2.0.3''| |
|[[orp-software|Oyster River Protocol]]|2.2.8|''module load orp/2.2.8''| |
|[[pagan-software|pagan]]|0.61|''module load pagan/0.61''| |
|[[pairfq-software|pairfq]]|0.14.4|''module load pairfq/0.14.4''| |
|[[paml-software|paml]]|4.9a|''module load paml/4.9a''| |
|[[panaroo-software|panaroo]]|1.3.3|''module load panaroo/1.3.3''| |
|[[pandaseq-software|pandaseq]]|2.8.1|''module load pandaseq/2.8.1''|  |
|[[pasta-software|pasta]]|d939adb2|''module load pasta/d939adb2''|  |
|[[pathoscope-software|pathoscope]]|2.0.7|''module load pathoscope/2.0.7''| |
|[[pear-software|pear]]|0.9.6|''module load pear/0.9.6''| |
|[[pblat-software|pblat]]|2.1|''module load pblat/2.1''| |
|[[pbsuite-software|pbsuite]]|15.8.24|''module load pbsuite/15.8.24''| |
|[[perl-software|perl]]|5.28.2|''module load perl/5.28.2''| |
|[[pgdspider-software|PGDSpider]]|2.1.1.0|''module load pgdspider/2.1.1.0''| |
|phrap|1.080812|''module load phrap/1.080812''| |
|phred|0.990722.f|''module load phred/0.990722.f''| |
|[[phylip-software|phylip]]|3.696|''module load phylip/3.696''| |
|[[phyml-software|phyml]]|3.3.20180621|''module load phyml/3.3.20180621''| |
|[[picard-software|picard]]|2.27.5|''module load picard/2.27.5''| |
|[[picrust-software#v1.0.0|picrust]]|1.0.0|''module load picrust/1.0.0''| |
|[[pilon-software|pilon]]|1.23|''module load pilon/1.23''| |
|[[plasmidid-software|plasmidid]]|1.6.5|''module load plasmidid/1.6.5''| |
|[[platanus-software|platanus]]|1.2.1|''module load platanus/1.2.1''| |
|[[plink-software|plink]]|2.00-alpha|''module load plink/2.00-alpha''| |
|[[pod5-software|pod5]]|0.3.2|''module load pod5/0.3.2''| |
|[[polyphen-software|polyphen]]|2.2.2|''module load polyphen/2.2.2''| |
|[[poplddecay-software|poplddecay]]|3.41|''module load poplddecay/3.41''| |
|[[porechop-software|porechop]]|0.3.2pre|''module load porechop/0.3.2pre''| |
|[[pplacer-software|pplacer]]|1.1.alpha19|''module load pplacer/1.1.alpha19''| |
|[[prank-software|prank]]|170427|''module load prank/170427''| |
|[[presto-software|presto]]|0.5.13|''module load presto/0.5.13''| |
|[[primalscheme-software|primalscheme]]|1.3.2|''module load primalscheme/1.3.2''| |
|primer3|2.3.6|''module load primer3/2.3.6''| |
|[[prinseq-software|prinseq]]|0.20.4|''module load prinseq/0.20.4''| |
|[[prodigal-software|prodigal]]|2.6.3|''module load prodigal/2.6.3''| |
|[[prokka-software|prokka]]|1.14.6|''module load prokka/1.14.6''| |
|[[provean-software|provean]]|1.1.5|''module load provean/1.1.5''| |
|[[purge-haplotigs-software|purge_haplotigs]]|1.1.1|''module load purge_haplotigs/1.1.1''| |
|[[python-software|python]]|3.9.17|''module load python/3.9''| |
|qdd|3_beta|''module load qdd/3_beta''| |
|[[qiime-software|qiime]]|1.9.1|''module load qiime/1.9.1''| |
|[[qiime2-software|qiime2]]|2021.8|''module load qiime2/2021.8''| |
|[[quast-software|quast]]|5.0.2|''module load quast/5.0.2''| |
|[[quickmerge-software|quickmerge]]|0.3|''module load quickmerge/0.3''| |
|[[quorum-software|Quorum]]|1.1.1|''module load quorum/1.1.1''| |
|[[r-software|R]]|4.3.1|''module load R/4.3''| |
|[[racon-software|racon]]|1.5.0|''module load racon/1.5.0''| |
|[[rapsearch-software|rapsearch]]|2.22|''module load rapsearch/2.22''| |
|[[ratt-software|RATT]]|r18|''module load ratt/r18''| |
|[[raxml-software|RAxML]]|8.2.12|''module load RAxML/8.2.12''| |
|[[ray-software|ray]]|2.3.1|''module load ray/2.3.1''| |
|[[rcorrector-software|rcorrector]]|1.0.5|''module load rcorrector/1.0.5''| |
|[[rdp-classifier-software|RDP Classifier]]|2.11|''module load rdp-classifier/2.11''| |
|[[recon-software|recon]]|1.08|''module load recon/1.08''| |
|[[repeatmasker-software|repeatmasker]]|4.1.2-p1|''module load repeatmasker/4.1.2-p1''| |
|[[repeatmodeler-software|repeatmodeler]]|2.0.1|''module load repeatmodeler/2.0.1''| |
|[[repseqio-software|repseqio]]|1.3.3|''module load repseqio/1.3.3''| |
|[[rgi-software|rgi]]|6.0.2|''module load rgi/6.0.2''| |
|[[rmblast-software|rmblast]]|2.11.0|''module load rmblast/2.11.0''| |
|[[roary-software|roary]]|3.13.0|''module load roary/3.13.0''| |
|[[root-software|root]]|6.08.06|''module load root/6.08.06''| |
|[[rrnaselector-software|rRNASelector]]|1.1|''module load rrnaselector/1.1''| |
|[[rsem-software|RSEM]]|1.3.1|''module load RSEM/1.3.1''| |
|[[rseqc-software|rseqc]]|2.6.4|''module load rseqc/2.6.4''| |
|[[ruby-software|ruby]]|3.1 (3.1.4)|''module load ruby/3.1''| |
|[[samtools-software|samtools]]|1.15.1|''module load samtools/1.15.1''| |
|[[sailfish-software|sailfish]]|0.9.2|''module load sailfish/0.9.2''| |
|[[salmon-software|salmon]]|1.3.0|''module load salmon/1.3.0''| |
|[[salsa-software|salsa]]|git-974589f3|''module load salsa/git-974589f3''| |
|[[satsuma2-software|satsuma2]]|git-37c5f386|''module load satsuma2/git-37c5f386''| |
|[[scipio-software|scipio]]|1.4.1|''module load scipio/1.4.1''| |
|[[scythe-software|scythe]]|0.994-beta|''module load scythe/0.994-beta''| |
|[[sepp-software|sepp]]|4.5.1|''module load sepp/4.5.1''| |
|[[seroba-software|seroba]]|1.0.0|''module load seroba/1.0.0''| |
|seq_crumbs|0.1.8|''module load seq_crumbs/0.1.8''| |
|[[seqkit-software|seqkit]]|0.11.0|''module load seqkit/0.11.0''| |
|[[seqqs-software|seqqs]]|git-3d053750|''module load seqqs/git-3d053750''| |
|[[seqtk-software|seqtk]]|1.3|''module load seqtk/1.3''| |
|[[seqwish-software|seqwish]]|0.6|''module load seqwish/0.6''| |
|[[shannon-software|shannon]]|0.0.2|''module load shannon/0.0.2''| |
|[[shannon_cpp-software|shannon_cpp]]|0.5.0|''module load shannon_cpp/0.5.0''| |
|[[shapeit-software|shapeit]]|2.904|''module load shapeit/2.904''| |
|[[shasta-software|shasta]]|0.4.0|''module load shasta/0.4.0''| |
|[[sickle-software|sickle]]|1.33|''module load sickle/1.33''| |
|[[sift-software|sift]]|4.0.3b|''module load sift/4.0.3b''| |
|[[sistr-software|sistr]]|1.0.2|''module load sistr/1.0.2''| |
|[[smalt-software|smalt]]|0.7.6|''module load smalt/0.7.6''| |
|[[smartdenovo-software|smartdenovo]]|git-5cc1356b|''module load smartdenovo/git-5cc1356b''| |
|[[snakemake-software|snakemake]]|6.15.5|''module load snakemake/6.15''| |
|[[sniffles-software|sniffles]]|1.0.12b|''module load sniffles/1.0.12b''| |
|[[snippy-software|snippy]]|4.6.0|''module load snippy/4.6.0''| |
|snowhite|1.1.4|''module load snowhite/1.1.4''| |
|[[snpeff-software|snpeff]]|5.1|''module load snpeff/5.1''| |
|[[snpmeta-software|snpmeta]]|2.0|''module load snpmeta/2.0''| |
|[[snp-pipeline-software|snp-pipeline]]|1.0.1|''module load snp-pipeline/1.0.1''| |
|[[soapdenovo2-software|SOAPdenovo2]]|git-c4d2f5ee|''module load SOAPdenovo2/git-c4d2f5ee''| |
|[[soapaligner-software|SOAPaligner]]|2.21|''module load SOAPaligner/2.21''| |
|[[soapsnp-software|SOAPsnp]]|1.03|''module load SOAPsnp/1.03''| |
|[[soapsplice-software|SOAPsplice]]|1.10|''module load SOAPsplice/1.10''| |
|[[soapdenovo-trans-software|SOAPdenovo-Trans]]|1.03|''module load SOAPdenovo-Trans/1.03''| |
|[[solexaqa-software|SolexaQA++]]|3.1.3|''module load SolexaQA++/3.1.3''| |
|[[spades-software|spades]]|3.15 (3.15.5)|''module load spades/3.15''| |
|[[sourmash-software|sourmash]]|1.0|''module load sourmash/1.0''| |
|[[speedseq-software|speedseq]]|0.1.2|''module load speedseq/0.1.2''| |
|splitstree|4.11.3|''module load splitstree/4.11.3''| |
|spread|1.0.6|''module load spread/1.0.6''| |
|[[squid-software|squid]]|1.9g|''module load squid/1.9g''| |
|[[sratoolkit-software|sratoolkit]]|2.10.0|''module load sratoolkit/2.10.0''| |
|[[sra-tools-software|sra-tools]]|3.0.0|''module load sra-tools/3.0.0''| |
|[[srprism-software|srprism]]|3.1.2|''module load srprism/3.1.2''| |
|[[srst2-software|srst2]]|git-73f885f5|''module load srst2/git-73f885f5''| |
|[[sspace-software|sspace]]|3.0|''module load sspace/3.0''| |
|[[sspace-longread-software|sspace-longread]]|1.1|''module load sspace-longread/1.1''| |
|[[stacks-software|stacks]]|2.62|''module load stacks/2.62''| |
|staden|2.0.0b8|''module load staden/2.0.0b8''| |
|[[star-software|star]]|2.7.10a|''module load star/2.7.10a''| |
|[[structure-software|structure]]|2.3.4|''module load structure/2.3.4''|  |
|[[stringtie-software|stringtie]]|1.3.4d|''module load stringtie/1.3.4d''| |
|[[stringtie2-software|stringtie2]]|2.2.1|''module load stringtie2/2.2.1''| |
|[[subread-software|subread]]|1.6.2|''module load subread/1.6.2''| |
|svmlight|V6.02|''module load svmlight/V6.02''| |
|tabix|git-76b4bbdf|''module load tabix/git-76b4bbdf''| |
|[[tablet-software|tablet]]|1.17.08.17|''module load tablet/1.17.08.17''| |
|[[tassel-software|tassel]]|5.2.77|''module load tassel/5.2.77''| |
|[[tmiseq-software|tmiseq]]|2016-01-31|''module load tmiseq/2016-01-31''| |
|[[tophat-software|tophat]]|2.1.0|''module load tophat2/2.1.0''| |
|[[tracer-software|tracer]]|1.6|''module load tracer/1.6''| |
|[[transabyss-software|transabyss]]|2.0.1|''module load transabyss/2.0.1''|  |
|[[transdecoder-software|TransDecoder]]|2.0.1|''module load TransDecoder/2.0.1''|  |
|[[transrate-software|Transrate]]|1.0.3|''module load transrate/1.0.3''|  |
|[[trf-software|trf]]|4.0.9|''module load trf/4.0.9''| |
|[[trimgalore-software|trimgalore]]|0.6.7|''module load trimgalore/0.6.7''| |
|[[trimmomatic-software|trimmomatic]]|0.39|''module load trimmomatic/0.39''| |
|[[trinity-software|trinity]]|v2.11.0|''module load trinity/v2.11.0''| |
|[[trinotate-software|trinotate]]|2.0.2|''module load trinotate/2.0.2''| |
|[[twinscan-software|twinscan]]|3.5|''module load twinscan/3.5''| |
|[[umi-tools-software|umi-tools]]| 0.2.3 |''module load umi-tools/0.2.3''| |
|[[unicycler-software|unicycler]]| 0.4.0 |''module load unicycler/0.5.0''| |
|[[usearch-software|usearch]]| v7.0.1090 |''module load usearch/v7.0.1090''| |
|varscan|2.4.2|''module load varscan/2.4.2''| |
|[[vcfdo-software|vcfdo]]|git-508cc19b|''module load vcfdo/git-508cc19b''| |
|[[vcflib-software|vcflib]]|git-7f1575e|''module load vcflib/git-7f1575e''| |
|[[vcftools-software|vcftools]]|0.1.16|''module load vcftools/0.1.16''| |
|[[velvet-software|velvet]]|1.2.10-kmer111|''module load velvet/1.2.10-kmer111''| |
|[[velvetoptimiser-software|velvetoptimiser]]|2.2.6|''module load velvetoptimiser/2.2.6''| |
|[[vep-software|vep]]|109.3|''module load vep/109.3''| |
|[[vg-software|vg]]|1.27.0|''module load vg/1.27.0''| |
|[[viennarna-software|viennarna]]|2.4.14|''module load viennarna/2.4.14''| |
|[[virusdetect-software|virusdetect]]|1.7|''module load virusdetect/1.7''| |
|[[vntrseek-software|vntrseek]]|1.08|''module load vntrseek/1.08''| |
|[[vsearch-software|vsearch]]|2.8.0|''module load vsearch/2.8.0''| |
|[[w2rap-software|w2rap]]|git-60781b6c|''module load w2rap/git-60781b6c''| |
|[[w2rap-contigger-software|w2rap-contigger]]|git-a43f5a05|''module load w2rap-contigger/git-a43f5a05''| |
|[[whatshap-software|whatshap]]|0.16|''module load whatshap/0.16''| |
|[[wise-software|wise]]|2.4.1|''module load wise/2.4.1''| |
|[[wombat-software|wombat]]|2020-02-07|''module load wombat/2020-02-07''| |
|[[wtdbg2-software|wtdbg2]]|2.4|''module load wtdbg2/2.4''| |

The source code for all environment modules can be found in [[https://github.com/ilri/hpc-environment-modules|ILRI's GitHub repository]].