QualiMap
Description
Qualimap is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.
License
Licensed under the Apache License, Version 2.0
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 qualiMap and load default version of qualiMap as
module avail qualiMap/ # list available modules module load qualiMap # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail qualiMap
and choose explicit version you want to use.
To enable graphic interface, option -X must be used when connecting via ssh e.g ssh -X meta_user@skirit.metacentrum.cz (see https://wiki.metacentrum.cz/wiki/Remote_desktop for details)
Documentation
http://qualimap.bioinfo.cipf.es/doc_html/index.html