---
name: "change_paired_read_orientation"
section: "1p"
platform: "linux"
package: "grinder"
version: "0.5.4-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/change_paired_read_orientation/1p"
---

# change\_paired\_read\_orientation(1p)

Change the orientation of paired-end reads in a FASTA file

## NAME

change\_paired\_read\_orientation - Change the orientation of paired-end reads in a FASTA file

## DESCRIPTION

Reverse the orientation, i.e. reverse-complement each right-hand paired-end read (ID ending in /2) in a FASTA file.

## REQUIRED ARGUMENTS

- \<in\_fasta\>

  FASTA file containing the reads to re-orient.

- \<out\_fasta\>

  Output FASTA file where to write the reads.

## COPYRIGHT

Copyright 2009-2012 Florent ANGLY \<florent.angly@gmail.com\>

Grinder is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License (GPL) as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. Grinder is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with Grinder.  If not, see \<http://www.gnu.org/licenses/\>.

## BUGS

All complex software has bugs lurking in it, and this program is no exception. If you find a bug, please report it on the SourceForge Tracker for Grinder: \<http://sourceforge.net/tracker/?group\_id=244196&atid=1124737\>

Bug reports, suggestions and patches are welcome. Grinder's code is developed on Sourceforge (\<http://sourceforge.net/scm/?type=git&group\_id=244196\>) and is under Git revision control. To get started with a patch, do:

```
   git clone git://biogrinder.git.sourceforge.net/gitroot/biogrinder/biogrinder
```