| name | diamond |
| description | Ultra-fast protein alignment (BLASTP/X alternative) for functional/taxonomic searches. Use this skill when working with diamond: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/bbuchfink/diamond. For stage routing use tool-selection / metagenomics-workflow.
|
| license | MIT |
| category | analysis-tools |
| tags | ["mapping","protein","blast"] |
| upstream | https://github.com/bbuchfink/diamond |
| stage | mapping |
DIAMOND
Upstream: DIAMOND
Citation
Buchfink, B., Reuter, K. & Drost, H.-G. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat. Methods 18, 366–368 (2021). https://doi.org/10.1038/s41592-021-01101-x
See also docs/references.md.
Analytical thinking
DIAMOND provides sensitive protein alignments at proteome/tree-of-life scale
(Buchfink et al., 2021) — the workhorse behind many functional and taxonomic
protein searches (eggNOG-mapper, DAS Tool protein search, custom NR/UniRef).
- Use
blastx/blastp for genes/proteins; not a substitute for nucleotide
coverage mappers (strobealign / bowtie2) needed for binning.
- Sensitivity modes (
--fast → --ultra-sensitive) trade speed for remote
homolog recall — state the mode in Methods.
- Tabular
-f 6 is pipeline-friendly; keep DB version pinned.
How to run
conda install -c bioconda diamond
diamond makedb --in proteins.faa -d ref
diamond blastp -q query.faa -d ref -o hits.tsv -p 16 -f 6
Key parameters
| blastp/blastx | mode | |
| -f 6 | tabular | BLAST-like |
Related skills
eggnog-mapper · mmseqs2 · blast · tool-selection · metagenomics-workflow
