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



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
$ git checkout v2.1.2
$ sudo mkdir -p /export/apps/kraken/2.1.2
$ sudo chown aorth /export/apps/kraken/2.1.2
$ ./ /export/apps/kraken/2.1.2
$ sudo chown root /export/apps/kraken/2.1.2/*

Download some pre-formatted databases and extract them somewhere:

$ sudo mkdir -p /export/data/bio/kraken2/db
$ wget
$ wget
$ wget
$ for name in *.tgz; do sudo tar xfv "$name" -C /export/data/bio/kraken2/db; done

Download the larger standard pre-formatted database:

$ wget
$ tar xf k2_standard_20210517.tar.gz
$ sudo mkdir -p /export/data/bio/kraken2/db/standard
$ sudo cp database* hash.k2d inspect.txt opts.k2d taxo.k2d /export/data/bio/kraken2/db/standard

The kraken2 application finds these with the KRAKEN2_DB_PATH environment variable.

kraken-software.txt · Last modified: 2022/07/07 11:27 by aorth