---
name: "fastaq-to_perfect_reads"
section: "1"
platform: "linux"
package: "fastaq"
version: "3.17.0-9"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fastaq-to_perfect_reads"
---

# fastaq-to\_perfect\_reads(1)

Make perfect paired reads from reference

## NAME

fastaq\_to\_perfect\_reads - Make perfect paired reads from reference

## DESCRIPTION

usage: fastaq\_to\_perfect\_reads \[options\] \<infile\> \<outfile\> \<mean insert size\> \<insert std deviation\> \<mean coverage\> \<read length\>

Makes perfect paired end fastq reads from a sequence 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 file

- outfile

  Name of output 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

### options:

- **-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