Kraken: Ultrafast metagenomic sequence classification using exact alignments

Derrick E. Wood, Steven L. Salzberg

Research output: Contribution to journalArticlepeer-review

1548 Scopus citations


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

Original languageEnglish (US)
Article numberR46
JournalGenome biology
Issue number3
StatePublished - Mar 3 2014


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

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology


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