====== kraken ======

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

===== Information =====

  * Version: 2.0.8-beta
  * Added: August, 2016
  * Updated: July, 2019
  * Link: https://ccb.jhu.edu/software/kraken2/

===== Usage =====

See which versions of kraken are available:
<code>$ module avail kraken</code>

Load one version into your environment and run it:
<code>$ module load kraken/2.0.8-beta
$ kraken2 --help</code>

===== Installation ======

Notes from the sysadmin during installation:

<code>$ git clone https://github.com/DerrickWood/kraken2.git
$ 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
$ ./install_kraken2.sh /export/apps/kraken/2.0.8-beta
$ sudo chown root /export/apps/kraken/2.0.8-beta/*</code>

Download some [[ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/|pre-formatted databases]] and extract them somewhere:

<code>$ sudo mkdir -p /export/data/bio/kraken2/db
$ wget ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/16S_Greengenes_20190418.tgz
$ wget ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken2_v1_8GB_201904_UPDATE.tgz
$ wget ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken2_v2_8GB_201904_UPDATE.tgz
$ for name in *.tgz; do sudo tar xfv "$name" -C /export/data/bio/kraken2/db; done</code>

The ''kraken2'' application finds these with the ''KRAKEN2_DB_PATH'' environment variable.