fastaq_scaffolds_to_contigs (1)

fastaq_scaffolds_to_contigs [options] <infile> <outfile>

Creates a file of contigs from a file of scaffolds - i.e. breaks at every gap in the input

positional arguments:

infile

Name of input fasta/q file

outfile

Name of output contigs file

optional arguments:

-h, --help

show this help message and exit

--number_contigs

Use this to enumerate contig names 1,2,3,... within each scaffold

fastaq_scaffolds_to_contigs 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.