kraken-software
Table of Contents
kraken
A taxonomic sequence classifier that assigns taxonomic labels to short DNA reads.
Information
- Version: 2.1.2
- Added: August, 2016
- Updated: July, 2022
Usage
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
Installation
Notes from the sysadmin during installation:
$ 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/*
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
Download the larger standard pre-formatted database:
$ wget https://genome-idx.s3.amazonaws.com/kraken/k2_standard_20210517.tar.gz $ 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 seqid2taxid.map 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