---
name: "fastaq_to_perfect_reads"
section: "1"
platform: "linux"
package: "fastaq"
version: "1.5.0-1"
release: "Debian 8 (Jessie)"
platforms: ["linux"]
url: "https://new.carta.tech/fastaq_to_perfect_reads"
---

# fastaq\_to\_perfect\_reads(1)

## NAME

fastaq\_to\_perfect\_reads

## DESCRIPTION

 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

## AUTHOR

fastaq\_to\_perfect\_reads was originally written by Martin Hunt (mh12@sanger.ac.uk)

## 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.