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

# fastaq\_extend\_gaps(1)

## NAME

fastaq\_extend\_gaps

## DESCRIPTION

 fastaq\_extend\_gaps \[options\] \<fasta/q in\> \<fasta/q out\>

Extends the length of all gaps (and trims the start/end of sequences) in a fasta/q file. Does this by replacing a set number of bases either side of each gap with Ns. Any sequence that ends up as all Ns is lost

### positional arguments:

- infile

  Name of input fasta/q file

- outfile

  Name of output fasta/q file

### optional arguments:

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

  show this help message and exit

- **--trim\_number** TRIM\_NUMBER

  Number of bases to trim around each gap, and off ends of each sequence \[100\]

## AUTHOR

fastaq\_extend\_gaps 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.