Kraken

module avail kraken/
module avail kraken2/

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.

Database

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 qsub requirement either 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.