kraken

A taxonomic sequence classifier that assigns taxonomic labels to short DNA reads.

• Version: 2.1.2
• Added: August, 2016
• Updated: July, 2022
• Link: https://ccb.jhu.edu/software/kraken2/

See which versions are available:

$ module avail kraken

Load one version into your environment and run it:

$ module load kraken/2.1.2
$ kraken2 --help

Notes from the sysadmin during installation:

$ cd /tmp
$ git clone https://github.com/DerrickWood/kraken2.git
$ git checkout v2.1.2
$ sudo mkdir -p /export/apps/kraken/2.1.2
$ sudo chown aorth /export/apps/kraken/2.1.2
$ ./install_kraken2.sh /export/apps/kraken/2.1.2
$ sudo chown root /export/apps/kraken/2.1.2/*

Download some pre-formatted databases and extract them somewhere:

$ cd /var/scratch
$ wget https://genome-idx.s3.amazonaws.com/kraken/16S_Greengenes13.5_20200326.tgz
$ wget https://genome-idx.s3.amazonaws.com/kraken/16S_Silva132_20200326.tgz
$ wget https://genome-idx.s3.amazonaws.com/kraken/16S_Silva138_20200326.tgz
$ for name in *.tgz; do sudo tar xfv "$name" -C /export/data/bio/kraken2/db; done

Download several larger databases (careful about space!):

$ wget https://genome-idx.s3.amazonaws.com/kraken/k2_standard_20230605.tar.gz
$ wget https://genome-idx.s3.amazonaws.com/kraken/k2_nt_20230502.tar.gz

The kraken2 application finds these with the KRAKEN2_DB_PATH environment variable.