Kraken2
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.
Licence
Public
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 kraken2 and load default version of kraken2 as
module avail kraken2/ # list available modules module load kraken2 # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail kraken2
and choose explicit version you want to use.
There is NT Kraken2 database available in shared location, in order to use it, run
kraken2 --db /storage/brno12-cerit/projects/Bio_databases/kraken2_nt_20230502
and request at least mem=500gb (unless only short query is processed with --memory-mapping option). For optimal performance of access to this database, we recommend adding another qsub requirement pbs_server=cerit-pbs.cerit-sc.cz or cluster=halmir (these select (two different sets of) machines with fastest network connection to the database storage).
Documentation
https://ccb.jhu.edu/software/kraken2/index.shtml?t=manual