Skip to content

Docs CSC now features an automatic Finnish translation. Click here for more information.

Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

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