GenomeTools

Description

The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules. Includes also the tool LTRdigest.

License

Free license based on OpenBSD model.

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 genometools and load default version of genometools as

module avail genometools/ # list available modules
module load genometools   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail genometools

and choose explicit version you want to use.

Documentation

http://genometools.org/documentation.html and http://www.zbh.uni-hamburg.de/?id=207. Except that is available the LTRdigest manual. When not on web anymore, use the local copy in directory /software/ltrdigest-1.5.1/docs.

Homepage

http://genometools.org and http://www.zbh.uni-hamburg.de/?id=207