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

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

===== Information =====

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

===== Usage =====

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

Load one version into your environment and run it:
<code>$ module load kraken/2.1.2
$ kraken2 --help</code>

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

Notes from the sysadmin during installation:

<code>$ 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/*</code>

Download some [[https://benlangmead.github.io/aws-indexes/k2|pre-formatted databases]] and extract them somewhere:

<code>$ 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</code>

Download several larger databases (careful about space!):

<code>$ 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</code>

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