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What is Kraken?

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 database of k-mer sequences from known genomes with established taxonomic relationships to perform its classifications.  

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