Diamond

Introduction

Diamond is sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data.

For more information, please check:

BioContainers: https://biocontainers.pro/tools/diamond

Home page: https://github.com/bbuchfink/diamond

Versions

• 2.0.15

• 2.1.6

Commands

• diamond

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run diamond on our clusters:

#!/bin/bash
#SBATCH -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=diamond
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load diamond/XXXX ### you can run *module avail diamond* to check all available versions

diamond makedb  --in uniprot_sprot.fasta -d uniprot_sprot
diamond blastp -p 24 -q test.faa -d uniprot_sprot  --very-sensitive -o blastp_output.txt