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kraken-software

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kraken

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

Information

Usage

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

Installation

Notes from the sysadmin during installation:

$ 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/*

Download some pre-formatted databases and extract them somewhere:

$ 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

The kraken2 application finds these with the KRAKEN2_DB_PATH environment variable.

kraken-software.txt · Last modified: 2019/07/15 20:04 by aorth