Seitenhistorie

Kraken

Kraken is a metagenomic mapping tool that calculates abundances of taxonomic labels in a mixed sample. To use it you can load the existing module kraken2/2.1.1 . For a pre-built database refer to the section below.

Demo call:

kraken2 --db /gpfs/project/databases/Kraken2_refseq+hfmv --threads 8 --report kraken.report myReads.fastq

Bracken

Bracken is a complementary tool for species level re-estimation and a compatible module is available: bracken/2.6.0.

Demo call:

est_abundance.py -i kraken.report -k /gpfs/project/databases/Kraken2_refseq+hfmv/kmerDistribution.txt -o bracken.report --out-report bracken.krakenstyle.report

Database

We have a shared database for Kraken2 available at

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