fastaq_to_perfect_reads1

Overview

fastaq_to_perfect_reads <fasta/q in> <out.fastq> <mean insert size> <insert std deviation> <mean coverage> <read length>

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.

positional arguments:

`infile`	Name of input fasta/q file
`outfile`	Name of output fastq file
`mean insert size`	Mean insert size of read pairs
`insert std deviation`	Standard devation of insert size
`mean coverage`	Mean coverage of the reads
`read length`	Length of each read

optional arguments:

-h, --help: show this help message and exit

--fragments FILENAME: Write FASTA sequences of fragments (i.e. read pairs plus sequences in between them) to the given filename

--no_n: Don't allow any N or n characters in the reads

--seed INT: Seed for random number generator. Default is to use python's default

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.