Diamond
Description
Diamond is a fast sequence similarity search tool for matching nucleotide or protein sequences against protein databases. The key features of Diamond are:
- Pairwise alignment of proteins and translated DNA at 500x-20,000x 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.
License
Free to use and open source under GNU AGPLv3.
Available
- Puhti: 2.0.15
Usage
To use Diamond, run first command:
module load biokit
diamond help
$DIAMONDDB
. For example searching hits for a set of nucleotide sequeces from the SwissProt database could be done with command:
diamond blastx --query nuc.fasta -d $DIAMONDDB/swiss --out diamond_results.txt -p 4 --max-target-seqs 500
diamond makedb --in refrerence_proteins.fasta -d my_ref -p 4
diamond blastx --query nuc.fasta -d my_ref --out diamond_results2.txt -p 4 --max-target-seqs 500
Manual Diamond Github page
Last update:
October 10, 2022