Trim Galore!
Description
A wrapper tool around Cutadapt to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.
License
GNU GPL v3 or later, https://www.gnu.org/copyleft/gpl.html
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of trim_galore and load default version of trim_galore as
module avail trim_galore/ # list available modules module load trim_galore # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail trim_galore
and choose explicit version you want to use.
(Program Cutadapt is made available automatically by the command above.)
List of all available options can be displayed using command
trim_galore --help
$ module add trim_galore-0.6.2
$ trim_galore [options] <filename(s)>
(Program Cutadapt is made available automatically by the command above.)
List of all available options can be displayed using command
trim_galore --help
Documentation
Official website: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
Official documentation (PDF): http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/trim_galore_User_Guide_v0.4.1.pdf
Homepage
http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/