NAME¶

fastaq_extend_gaps

DESCRIPTION¶

fastaq_extend_gaps [options] <fasta/q in> <fasta/q out> Extends the length of all gaps (and trims the start/end of sequences) in a fasta/q file. Does this by replacing a set number of bases either side of each gap with Ns. Any sequence that ends up as all Ns is lost

positional arguments:¶

infile

Name of input fasta/q file

outfile

Name of output fasta/q file

optional arguments:¶

-h, --help

show this help message and exit

--trim_number TRIM_NUMBER

Number of bases to trim around each gap, and off ends of each sequence [100]

AUTHOR¶

fastaq_extend_gaps was originally written by Martin Hunt (mh12@sanger.ac.uk)

COPYING¶

Wellcome Trust Sanger Institute Copyright © 2013 Wellcome Trust Sanger Institute This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.