diamond
Diamond is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. 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
Link to section 'Versions' of 'diamond' Versions
- 2.0.13
- 2.0.14
- 2.0.15
Link to section 'Commands' of 'diamond' Commands
- diamond makedb
- diamond prepdb
- diamond blastp
- diamond blastx
- diamond view
- diamond version
- diamond dbinfo
- diamond help
- diamond test
Link to section 'Module' of 'diamond' Module
You can load the modules by:
module load biocontainers
module load diamond/2.0.14
Link to section 'Example job' of 'diamond' Example job
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 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