Software: Diamond
Description
Diamond is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data.
Available Versions
| Unspecified: | 2.0.13 2.0.14 2.0.15 2.1.6 |
|---|
The key features are:
- Pairwise alignment of proteins and translated DNA at 100x-10,000x speed of BLAST.
- Frameshift alignments for long read analysis.
- Low resource requirements and suitable for running on standard desktops or laptops.
- Various output formats, including BLAST pairwise, tabular and XML, as well as taxonomic classification.
Detailed about its usage can be found here: https://github.com/bbuchfink/diamond
Commands
- diamond makedb
- diamond prepdb
- diamond blastp
- diamond blastx
- diamond view
- diamond version
- diamond dbinfo
- diamond help
- diamond test
Module
You can load the modules by:
module load biocontainers
module load diamond/2.0.14
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
To run diamond on our our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=diamond
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers diamond/2.0.14
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