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Kraken

Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.

Kraken is available as a module on Apocrita.

Usage

To run the latest installed version of Kraken, simply load the kraken module:

module load kraken

For usage documentation, run kraken -h.

Example job

Serial job

Here is an example job running on 1 core and 5GB total memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=5G

module load kraken

kraken --db example_db \
       --threads ${NSLOTS} \
       input_file

References