Run BLAST

Description

This script runs BLAST on a given set of query files.

Input files

• optional: query files (.fa | .faa | .fas | .fasta)
• at least 1 database file (.phr | .pin | .psq)

Output files

• CSV BLAST results (blast-results.csv)

Context

General parameters

BLAST program

Choices: blastp (default), psi-blast, phi-blast

Word size

Default: 0

E-value threshold

Default: 10.0

Scoring parameters

Matrix

Choices: PAM30, PAM70, BLOSUM80, BLOSUM62 (default), BLOSUM45

Gap opening cost

Default: -1

Gap extension cost

Default: -1

Filters and Masking

Filter low complexity regions

Choices: yes (default), no

Tweaks

Number of CPU cores to use

Default: 1

Additional parameters

Peptides

Default: empty

Source code

run-blast.rb, run-blast.yaml (GitHub)