.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH FASTAQ_TO_PERFECT_READS "1" "October 2014" "Fastaq" "Fastaq executables"
.SH NAME
fastaq_to_perfect_reads
.SH DESCRIPTION
 fastaq_to_perfect_reads <fasta/q in> <out.fastq> <mean insert size> <insert std deviation> <mean coverage> <read length>
.PP
Makes perfect paired end fastq reads from a fasta/q file, with insert sizes
sampled from a normal distribution. Read orientation is innies. Output is an
interleaved fastq file.
.SS "positional arguments:"
.TP
infile
Name of input fasta/q file
.TP
outfile
Name of output fastq file
.TP
mean insert size
Mean insert size of read pairs
.TP
insert std deviation
Standard devation of insert size
.TP
mean coverage
Mean coverage of the reads
.TP
read length
Length of each read
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-fragments\fR FILENAME
Write FASTA sequences of fragments (i.e. read pairs
plus sequences in between them) to the given filename
.TP
\fB\-\-no_n\fR
Don't allow any N or n characters in the reads
.TP
\fB\-\-seed\fR INT
Seed for random number generator. Default is to use
python's default


.SH "AUTHOR"
.sp
fastaq_to_perfect_reads 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\&.