Main tool: diamond
Code repository: https://github.com/bbuchfink/diamond
Additional tools:
- ncbi-blast+ : 2.12.0
Basic information on how to use this tool:
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executable: diamond
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help: help
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version: version
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description: 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.
- Protein clustering of up to tens of billions of proteins
- 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.
Full documentation: https://github.com/bbuchfink/diamond/wiki
# Protein alignment
diamond makedb --in proteins.fa -d db
diamond blastp -q query.fa -d db -o out.tsv --very-sensitive
# Protein clustering
diamond cluster -d proteins.fa -o clusters.tsv --approx-id 40 -M 12G --header