fastaq_extend_gaps(1) extends the length of all gaps in a fasta/q file


 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:

Name of input fasta/q file
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]


fastaq_extend_gaps was originally written by Martin Hunt ([email protected])


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.