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Bracken: Estimating species abundance in metagenomics data

View ORCID ProfileJennifer Lu, Florian P Breitwieser, Peter Thielen, Steven L Salzberg
doi: https://doi.org/10.1101/051813
Jennifer Lu
1Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD
2Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine
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  • ORCID record for Jennifer Lu
  • For correspondence: jlu26@jhmi.edu fbreitw1s@jhu.edu peter.thielen@jhuapl.edu salzberg@jhu.edu
Florian P Breitwieser
2Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine
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Peter Thielen
3Applied Physics Laboratory, Johns Hopkins University
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Steven L Salzberg
1Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD
2Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine
4Departments of Computer Science and Biostatistics, Johns Hopkins University
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Abstract

We describe a new, highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN) uses the taxonomy labels assigned by Kraken, a highly accurate metagenomics classification algorithm, to estimate the number of reads originating from each species present in a sample. Kraken classifies reads to the best matching location in the taxonomic tree, but does not estimate abundances of species. We use the Kraken database itself to derive probabilities that describe how much sequence from each genome is shared with other genomes in the database, and combine this information with the assignments for a particular sample to estimate abundance at the species level, the genus level, or above. Combined with the Kraken classifier, Bracken produces accurate species-and genus-level abundance estimates even when a sample contains multiple near-identical species.

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Posted May 05, 2016.
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Bracken: Estimating species abundance in metagenomics data
Jennifer Lu, Florian P Breitwieser, Peter Thielen, Steven L Salzberg
bioRxiv 051813; doi: https://doi.org/10.1101/051813
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Bracken: Estimating species abundance in metagenomics data
Jennifer Lu, Florian P Breitwieser, Peter Thielen, Steven L Salzberg
bioRxiv 051813; doi: https://doi.org/10.1101/051813

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