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Kraken is a taxanomic sequence classifier that assigns taxonomic labels to short DNA sequences, typically from microbiome or metagenomic studies (1). Kraken classifies reads to a best-match location in a taxonomic tree (the lowest common ancestor), so not all sequences will be classified to a particular level such as species. Kraken matches k-mers (nucleotide sequences of k bases in length) within a read to a database of k-mer sequences from known genomes with established taxonomic relationships to perform its classifications.  Partek Flow currently wraps Kraken version 2 (1)..0.8-beta (2), but Kraken 0.10.5-beta is also available (to roll back to the older version, see Task Management).

Running Kraken

Kraken takes FASTQ files as input. Reads can be single- or paired-end.

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Kraken generates a Taxonomic data node. This data can be used as input for the Alpha & Beta diversity and Choose taxonomic level tasks. If you want to obtain the Kraken output files, select the new data node and choose Download data from the toolbox on the right. 

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