Enveomics collection

A toolbox for microbial genomics and metagenomics

BlastTab.catsbj.pl

Generates a list of hits from a BLAST result concatenating the subject sequences. This can be used, e.g., to analyze BLAST results against draft genomes. This script creates two files using <map.bls> as prefix with extensions .rec (for the recruitment plot) and .lim (for the limits of the different sequences in <seq.fa>).

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

§ Usage

BlastTab.catsbj.pl [opts] in_file in_file

§ Arguments

Identity
 -i float  Minimum identity (in %) to report a result.
Length
 -l float  Minimum alignment length to report a result.
Subset
 -s   The FastA provided is to be treated as a subset of the subject. By default, it expects all the BLAST subjects to be present in the FastA.
Quiet
 -q   Run quietly.
seq.fa*
 in_file  Subject sequences (ref) in FastA format.
map.bls*
 in_file  Mapping of the reads to the reference in Tabular BLAST format.
* Mandatory.