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



See which versions of kraken are available:

$ module avail kraken

Load one version into your environment and run it:

$ module load kraken/2.0.8-beta
$ kraken2 --help


Notes from the sysadmin during installation:

$ git clone
$ cd kraken2
$ git checkout v2.0.8-beta
$ sudo mkdir -p /export/apps/kraken/2.0.8-beta
$ sudo chown aorth /export/apps/kraken/2.0.8-beta
$ ./ /export/apps/kraken/2.0.8-beta
$ sudo chown root /export/apps/kraken/2.0.8-beta/*

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

The kraken2 application finds these with the KRAKEN2_DB_PATH environment variable.

kraken-software.txt · Last modified: 2019/07/15 17:04 by aorth