Farm_blast

Python3 module to run blast+ or blastall in parallel on an LSF compute farm

Installation

Prerequisites:

• NCBI BLAST NCBI BLAST blast+, and optionally blastall, installed and their commands in your path

Once the prerequisites are installed, install with pip:

pip3 install farm_blast

Synopsis

Compare a query and a reference using blast+ blastn:

farm_blast reference.fasta query.fasta

Compare a query and a reference using blastall blastn:

farm_blast --blastall reference.fasta query.fasta

Run blast+ megablast:

farm_blast --blast_type megablast reference.fasta query.fasta

Run blastall tblastx:

farm_blast --blast_type tblastx --blastall reference.fasta query.fasta

Set the e-value and word length and do not filter the query sequence:

farm_blast --no_filter -e 0.1 -W 30 reference.fasta query.fasta

To get all the options, use --help:

farm_blast --help