Kraken2 is a bioinformatics tool originally designed for metagenomic applications. It has additionally proven valuable for validating taxonomic assignments and checking contamination of single-species (e.g. bacterial isolate, eukaryotic isolate, viral isolate, etc.) whole genome sequence data.

There are two Kraken2 workflows:

Kraken2_PE is compatible with Illumina paired-end data
Kraken2_SE is compatible with Illumina single-end data
Kraken2_ONT is compatible with Oxford Nanopore data

Besides the data input types, there are minimal differences between these two workflows.

Page Contents

Workflows available

Databases

Inputs

Outputs

References