CHANGE_PAIRED_READ_ORIENTATION(1)

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