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

# fastaq\_sequence\_trim(1)

## NAME

fastaq\_sequence\_trim

## DESCRIPTION

 fastaq\_sequence\_trim \[options\] \<fasta/q 1 in\> \<fastaq/2 in\> \<out 1\> \<out 2\> \<trim\_seqs\>

Trims sequences off the start of all sequences in a pair of fasta/q files, whenever there is a perfect match. Only keeps a read pair if both reads of the pair are at least a minimum length after any trimming

### positional arguments:

- fasta/q 1 in

  Name of forward fasta/q file to be trimmed

- fasta/q 2 in

  Name of reverse fasta/q file to be trimmed

- out\_1

  Name of output forward fasta/q file

- out\_2

  Name of output reverse fasta/q file

- trim\_seqs

  Name of fasta/q file of sequences to search for at the start of each input sequence

### optional arguments:

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

  show this help message and exit

- **--min\_length** INT

  Minimum length of output sequences \[50\]

## AUTHOR

fastaq\_sequence\_trim 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.