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Diamond

Diamond is a fast sequence similarity search tool for matching nucleotide or protein sequences against protein databases. It aligns proteins and translated DNA at 100–10,000× the speed of BLAST, supports frameshift alignments for long-read analysis, runs with low resource requirements, and writes a range of output formats (BLAST pairwise, tabular, XML, and taxonomic classification).

License

Free to use and open source under GNU GPLv3.

Available

  • Roihu-CPU: 2.1.10 (module diamond), via the bio-apps module.

Usage

Diamond is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the Diamond module:

module load bio-apps/v202603
module load diamond/2.1.10

After that, you can check the Diamond help with the command:

diamond help

Reference databases

CSC provides shared Diamond indexes for the NCBI non-redundant (nr) and SwissProt (swiss) protein databases. The diamond module sets the environment variable $DIAMONDDB to their location, and you refer to an index by basename (Diamond appends .dmnd). For example, searching a set of nucleotide sequences against SwissProt:

diamond blastx --query nuc.fasta -d $DIAMONDDB/swiss --out diamond_results.txt -p 4 --max-target-seqs 500

nr is very large, so a search against it (-d $DIAMONDDB/nr) needs substantial memory and time — reserve them accordingly.

Using your own database

You can also search against your own protein sequence database. First build a Diamond index for your reference protein set with diamond makedb:

diamond makedb --in reference_proteins.fasta -d my_ref -p 4

The command above creates a Diamond index file (my_ref.dmnd) that can be used as the query database:

diamond blastx --query nuc.fasta -d my_ref --out diamond_results2.txt -p 4 --max-target-seqs 500

More information