kraken2

Kraken2 subworkflow

kraken2 is a useful tool for identification of possible inter-species contamination. The kraken2 subworkflow is an optional workflow that requires a kraken2 database. Instructions on how to download a Kraken2 database can be found on a different wiki page.

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kraken2
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flowchart LR
fastq --> kraken2
database --> kraken2

Loading

Relevant params with their default values:

params.kraken2_db = ""