Kraken2¶
Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
Kraken2 is available as a module on Apocrita.
Usage¶
To run the default installed version of Kraken2, simply load the kraken2
module:
module load kraken2
For usage documentation, run kraken2 -h.
Example job¶
Serial job¶
Here is a Kraken2 example job running on 1 core and 5GB of memory:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=5G
module load kraken2
kraken2 --db example2_db \
--threads ${NSLOTS} \
input_file