.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH FASTAQ_SCAFFOLDS_TO_CONTIGS "1" "October 2014" "Fastaq" "Fastaq executables"
.SH NAME
fastaq_scaffolds_to_contigs
.SH DESCRIPTION
 fastaq_scaffolds_to_contigs [options] <infile> <outfile>
.PP
Creates a file of contigs from a file of scaffolds \- i.e. breaks at every gap
in the input
.SS "positional arguments:"
.TP
infile
Name of input fasta/q file
.TP
outfile
Name of output contigs file
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-number_contigs\fR
Use this to enumerate contig names 1,2,3,... within each
scaffold


.SH "AUTHOR"
.sp
fastaq_scaffolds_to_contigs was originally written by Martin Hunt (mh12@sanger.ac.uk)

.SH "COPYING"
.sp
Wellcome Trust Sanger Institute Copyright \(co 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\&.