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diamond container

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:

  • executable: diamond

  • help: help

  • version: version

  • 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

Example Usage

# 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