Kraken2

Kraken2 is the second iteration of Kraken and is not compatible with Kraken1. Meant for ultra fast and highly accurate assigning taxonomic labels to metagenomic DNA sequences, it utilizes the kraken2 databases that we have installed on palmetto. See our Public Databases to see how to find those databases.

To load Kraken2 on to Palmetto 2:

module load biocontainers
module load kraken2

An example analysis command would look roughly:

kraken2 -db <appropriate databases> --threads NUM_THREADS --report REPORT.txt INPUT.fa > OUTPUT.kraken

tip

This software has multithreading features! Please try to request additional resources to expedite your analyses! Remember to set the --threads flag accordingly!

Please see Oregon's Kraken2 guide for more information about Kraken2.

Parallel Capabilities: Multithreading options available.