Kraken: ultrafast metagenomic sequence classification using exact alignments
Open accessAbstract
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 http://ccb.jhu.edu/software/kraken/.
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- Authors
- Wood, D. E., & Salzberg, S. L.
- Affiliations
- Johns Hopkins University (US)
- Corresponding author
- Wood, Derrick E
- Venue
- Genome Biology
- Published
- 2014-03-03
- Volume
- 15
- Issue
- 3
- Pages
- R46-R46
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC4053813
- OpenAlex
- W2159954944
- Semantic Scholar
- 7bbac7f7916567616d933d4b2fc8b8acbbb51bdc
- Cited by
- 4,521
- References
- 23
- Citations by year
- 2026: 298 · 2025: 453 · 2024: 479 · 2023: 449 · 2022: 433 · 2021: 572 · 2020: 550 · 2019: 440 · 2018: 337 · 2017: 227 · 2016: 166 · 2015: 84 · 2014: 28
- FWCI
- 68.77
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Zenodo (CERN European Organization for Nuclear Research) (submittedVersion, cc-by)
- Funders
- National Institutes of Health
- National Human Genome Research Institute (R01HG006677)
- National Institute of General Medical Sciences (R01GM083873)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- metagenomic sequence classification, taxonomic classification, metagenomics, BLAST comparison, Kraken
- MeSH terms
- Archaea, Bacteria, Classification, Humans, Sensitivity and Specificity, Software, Sequence Alignment, Sequence Analysis, DNA, Metagenome, Metagenomics
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