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Table of Contents
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
- Latest Version: 0.9.9
- Added: November, 2016
- Updated: July, 2017
Usage
See which versions of diamond are available:
$ module avail diamond
Load the diamond environment module and run it:
$ module load diamond/0.9.9 $ diamond
An example SLURM submission script might look like:
#!/bin/env bash #SBATCH -p batch #SBATCH -n 4 #SBATCH -J diamond # Load diamond module module load diamond/0.9.9 # Set up environment export DATADIR=/home/aorth/data export WORKDIR=/var/scratch/aorth/diamond-2017-08-17 # Create and change to working directory mkdir -p $WORKDIR cd $WORKDIR diamond blastx -p 4 -q $DATADIR/test_nt_seq.fa --sensitive -d /export/data/bio/diamond/nr -o test_nt_seq.xml -f 5
Make sure to match the number of CPUs in your SLURM request (-n
) with the amount in your diamond command line (-p
).
Installation
Notes from the sysadmin during installation:
$ cd /tmp $ wget https://github.com/bbuchfink/diamond/releases/download/v0.9.9/diamond-linux64.tar.gz $ tar xf diamond-linux64.tar.gz $ sudo cp diamond diamond_manual.pdf /export/apps/diamond/0.9.9
Diamond requires specially formatted databases, which you create using the diamond makedb
subcommand. The input must be a FASTA file, but can be gzip compressed, for example the NR database from NCBI:
$ wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz $ diamond makedb --in nr.gz -d nr $ sudo mkdir -p /export/data/bio/diamond $ sudo cp nr.dmnd /export/data/bio/diamond