sgivan / clusterblast

Tools for running and parsing emabarrasingly parallel NCBI BLAST jobs

clusterblast

Scripts for running and parsing emabarrasingly parallel NCBI BLAST jobs

Dependencies that may not already be installed on your system:

• BioPerl
• Moose

Summary

The clusterblast script includes a fairly good help message that covers command line options. To see the help message, run:

>clusterblast -h

This is a script that takes a FASTA-formatted file of nucleotide
or protein sequences and BLASTs them using the Slurm scheduler.
A summary of the command line options:

usage: clusterblast -f <folder name> -d <blast database name> -b <blast program>

-f      FASTA file name
-d      the BLAST database to search
-b      the type of BLAST program (ie, blastn, blastp)
-P      path to blast database, if not /dfs/databases/ (use '/' as last character)
-B      use the new family of NCBI BLAST binaries (not blastall)
-n      contig number cutoff (seq name must be in form Contig###)
-l      minimum sequence length to accept [1]
-L      maximum sequence length to accept [1000000]
-a      extra arguments to send to blastall (ie, -a '-b 500', or '-num_alignments 500')
-r      amount of RAM needed by blastall (default = 10G)
-E      BLAST E-value cut-off (defaults to 1e-06; enclose in quotes)
-H      generate HTML output
-M      use Megablast (only available for a blastn search)
-q      which Slurm partition to submit the jobs to [CLUSTER]
-p      number of processors to use per blast job [1]
-N      specific nodes to run jobs on; for example:
            -N 'chrom10-20'
            -N 'chrom10-20;chrom40-52'
            -N 'chrom10;chrom12;chrom15'
            -N 'chrom10;chrom12-15;chrom18'
-h      display this help message
-Q      quite mode
-W      after submitting jobs, don't wait for them to finish before exiting
-c #    throttle queue submission (pause after this number of job submissions)
-D      debug mode -- don't submit jobs to cluster

The bestblastparse.pl script parses the output of clusterblast and generates a spreadsheet-style summary file. It also has a help message:

>bestblastparse.pl -h

This script takes a collection of BLAST result files and parses
out all of the hits above a user-selected E-value.  It sends
the output to a tab-delimited file.

 usage:  bestblastparse -f <file name>

Option  Description
 -f     input folder name
 -M     use this flag if clusterblastmax was used
 -o     output file name (defaults to bestblast.tab)
 -e     E-value cutoff (defaults to 1e-06)
 -p     % identity cutoff (85 means 85%)
 -c     queue coverage cutoff (percentage; ie 85 means 85%)
 -C     subj coverage cutoff (percentage; ie 85 means 85%. Requires -d also)
 -t     output statistics for tiled hsps
 -E     print report for every hit < E-value (overrides -n)
 -l     generate output for every ORF (even with no hits)
 -b     type of blast search [defaults to blastn]
 -n     number of best hits to output for each report
 -d     print detailed information about best hit
 -a     print alignment for each hit
 -S     name of file to print summary information
 -q     quiet mode
 -h     display this help message