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 2. See our Public Databases to see how to find those databases.

Using the module

To load Kraken2 on Palmetto 2:

module load biocontainers
module load kraken2

After loading the biocontainers module, you can see the available commands by running:

report_subtools.sh kraken2

Example

An example analysis command would look roughly:

kraken2 -db <appropriate databases> --threads $SLURM_CPUS_ON_NODE --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 Derrick Wood's Kraken2 guide for more information about Kraken2.

Parallel Capabilities: Multithreading options available.