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 an nt Kraken2 database available in a shared location. In order to use it, run

kraken2 --db /storage/brno12-cerit/projects/Bio_databases/kraken2_nt_20240530
# includes the NCBI Taxonomy database

# older releases:  
# /storage/brno12-cerit/projects/Bio_databases/kraken2_nt_20230502

and request at least mem=890gb for kraken2_nt_20240530 database (unless only a short query is processed with the --memory-mapping option) or mem=520gb for kraken2_nt_20230502 database (unless only a short query is processed with the --memory-mapping option).

For optimal performance of access to this database, we recommend adding qsub requirement cluster=halmir. This selects machines with the fastest network connection to the database storage.