Releasing the Kraken

Steven L Salzberg; Derrick E Wood

doi:10.3389/fbinf.2021.808003

Releasing the Kraken

Front Bioinform. 2021 Dec 6:1:808003. doi: 10.3389/fbinf.2021.808003. eCollection 2021.

Authors

Steven L Salzberg^{1

2

3

4}, Derrick E Wood^{2

3}

Affiliations

¹ Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States.
² Center for Computational Biology, Johns Hopkins University, Baltimore, MD, United States.
³ Department of Computer Science, Johns Hopkins University, Baltimore, MD, United States.
⁴ Department of Biostatistics, Johns Hopkins University, Baltimore, MD, United States.

Abstract

Ten years ago, the dramatic rise in the number of microbial genomes led to an inflection point, when the approach of finding short, exact matches in a comprehensive database became just as accurate as older, slower approaches. The new idea led to a method that was hundreds of times times faster than those that came before. Today, exact k-mer matching is a standard technique at the heart of many microbiome analysis tools.

Keywords: k-mer matching; metagenomics; microbiome; phylogenetic classification; sequence alignment; sequencing indexing.

Abstract

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