Run BLAST
Contents
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)