Kraken

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Description

Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.

License

GNU GPL

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 kraken and load default version of kraken as

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


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

module avail kraken

and choose explicit version you want to use.

Documentation

https://github.com/DerrickWood/kraken2/wiki/Manual

Homepage

https://ccb.jhu.edu/software/kraken2/