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

# fastaq\_long\_read\_simulate(1)

## NAME

fastaq\_long\_read\_simulate

## DESCRIPTION

 fastaq\_long\_read\_simulate \[options\] \<infile\> \<outfile\>

Simulates long reads from a fasta/q file. Can optionally make insertions into the reads, like pacbio does. If insertions made, coverage calculation is done before the insertions (so total read length may appear longer then expected).

### positional arguments:

- infile

  Name of input fasta/q file

- outfile

  Name of output fasta file

### optional arguments:

- **-h**, **--help**

  show this help message and exit

- **--method** tiling\|uniform\|gamma

  How to sample the read positions and lengths. Choose from 1) "tiling", where reads of fixed length are taken at equal intervals from the reference. 2) "unfiform", where reads of fixed length taken at positions sampled uniformly. 3) "gamma", where reads lengths are taken from a gamma distribution, and positions sampled uniformly. \[tiling\]

- **--seed** INT

  Seed for random number generator \[default: use python's default\]

- **--qual** INT

  Write a file of fake quality scores called outfile.qual, all bases same quality \[None\]

- **--fixed\_read\_length** INT

  Length of each read. Only applies if method is tile or uniform. \[20000\]

- **--coverage** FLOAT

  Read coverage. Only applies if method is gamma or uniform. \[2\]

### tiling options:

- **--tile\_step** INT

  Distance between start of each read \[10000\]

### gamma options:

- **--gamma\_shape** FLOAT

  Shape parameter of gamma distribution \[1.2\]

- **--gamma\_scale** FLOAT

  Scale parameter of gamma distribution \[6000\]

- **--gamma\_min\_length** INT

  Minimum read length \[20000\]

### options to add insertions to reads:

- **--ins\_skip** INT

  Insert a random base every **--skip** bases plus or minus **--ins\_window**. If this option is used, must also use **--ins\_window**.

- **--ins\_window** INT

  See **--ins\_skip**. If this option is used, must also use **--ins\_skip**.

## AUTHOR

fastaq\_long\_read\_simulate 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.