KAT
Description
KAT provides a suite of tools that, through the use of k-mer counts, help the user address or identify issues such as determining sequencing completeness for assembly, assessing sequencing bias, identifying contaminants, validating genomic assemblies and filtering content. KAT is geared primarily to work with high-coverage genomic reads from Illumina devices, although can work with any fasta or fastq sequence file.
License
http://www.gnu.org/licenses/gpl.txt
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 kat and load default version of kat as
module avail kat/ # list available modules module load kat # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail kat
and choose explicit version you want to use.
Documentation
http://kat.readthedocs.io/en/latest/index.html