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Kraken: ultrafast metagenomic sequence classification using exact alignments

Derrick E Wood12* and Steven L Salzberg23

Author Affiliations

1 Department of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA

2 Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA

3 Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA

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Genome Biology 2014, 15:R46  doi:10.1186/gb-2014-15-3-r46

Published: 3 March 2014


Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. Using exact alignment of k-mers, Kraken achieves classification accuracy comparable to the fastest BLAST program. In its fastest mode, Kraken classifies 100 base pair reads at a rate of over 4.1 million reads per minute, 909 times faster than Megablast and 11 times faster than the abundance estimation program MetaPhlAn. Kraken is available at webcite.

metagenomics; sequence classification; sequence alignment; next-generation sequencing; microbiome