NAME

        runParallelBlast.pl - Run BLAST on clusters.

Splits a query file into small files, submits to the cluster and combines the results.

SYNOPSIS

        runParallelBlast.pl [options]

--flavor=name: WU-BLAST (WU), NCBI-BLAST (NCBI) or NCBI-BLAST+ (NCBI+) flavors of BLAST
--blast=program: BLAST program (blastn|blastp|blastx|tblastn|tblastx)
--database=prefix: name of the blast database file
--query=file: query file
--label=name: Output file will be stored as <out_dir>/<label>.<program>
--outdir=dir: directory to store the output file
--splitsize=num: (approximate) number of basepairs in each smaller query file
--outfmt=format: NCBI tabular output format string (default: \"7 std\")
--help: print this help

--wordsize=num: Word size for BLAST seeding step (default: BLAST defaults)
--evalue=num: E-value threshold for results to be included, passed to blast (default: 0.1)
--subjects=num: maximum number of subjects per query to report, passed to blast (default: 1000)
--notabular: disable tabular output of BLAST (default: enabled) --notabular only works when --pieces=1
--extra_args=string: additional arguments passed to blast as they are (use quotes if you use multiple parameters)
--cpus=num: number of cpus to use for every subjob (default: 1)
--stage=mode: local staging location (memory or tmp) in the node to copy the blast database (default: tmp)

--bits=num: bit threshold for results to be included (default: none)
--preprocessor=command: pre processing command. For example, if you want to blast to be run by a another script that takes blast commands as argument (such as MPblast), then you should run it as:; This will make a final command such as:
--postprocessor=command: post processing command. For example, if you want to blast output through a script that performs conversion to cigar format, then you should run it as:; This will make a final command such as: