ILRI Research Computing

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====== 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
  * Updated: March, 2022
  * Link: https://github.com/bbuchfink/diamond
  
===== Usage =====

See which versions are available:
<code>$ module avail diamond</code>

Load one version into your environment and run it:
<code>$ module load diamond/2.0.14
$ diamond</code>

An example SLURM submission script might look like:

<code>#!/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</code>

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:

<code>$ cd /tmp
$ wget http://github.com/bbuchfink/diamond/releases/download/v2.0.14/diamond-linux64.tar.gz
$ sudo mkdir -p /export/apps/diamond/2.0.14/bin
$ tar xf diamond-linux64.tar.gz
$ sudo cp diamond /export/apps/diamond/2.0.14/bin</code>

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:

<code>$ wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz
$ wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.FULL.gz
$ wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip
$ unzip taxdmp.zip
$ diamond makedb --in nr.gz --db nr --taxonmap prot.accession2taxid.FULL.gz --taxonnodes nodes.dmp --taxonnames names.dmp
$ sudo mkdir -p /export/data/bio/diamond
$ sudo cp nr.dmnd /export/data/bio/diamond</code>