Bracken: estimating species abundance in metagenomics data

Metagenomic experiments attempt to characterize microbial communities using high-throughput DNA sequencing. Identification of the microorganisms in a sample provides information about the genetic profile, population structure, and role of microorganisms within an environment. Until recently, most me...

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Published inPeerJ. Computer science Vol. 3; p. e104
Main Authors Lu, Jennifer, Breitwieser, Florian P., Thielen, Peter, Salzberg, Steven L.
Format Journal Article
LanguageEnglish
Published United States PeerJ. Ltd 02.01.2017
PeerJ, Inc
PeerJ Inc
Subjects
Abundance
Analysis
Bacteria
Bayesian analysis
Bayesian estimation
Deoxyribonucleic acid
DNA
DNA sequencing
Estimation
Gene sequencing
Genomes
Medical research
Metagenomics
Methods
Microbial populations
Microbiome
Microorganisms
Ribonucleic acid
Ribosomal RNA
RNA
Species abundance
Taxonomy
Tuberculosis
Metagenomics
Bayesian estimation
Species abundance
Bioinformatics
Computational Biology
Microbiome
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Summary:Metagenomic experiments attempt to characterize microbial communities using high-throughput DNA sequencing. Identification of the microorganisms in a sample provides information about the genetic profile, population structure, and role of microorganisms within an environment. Until recently, most metagenomics studies focused on high-level characterization at the level of phyla, or alternatively sequenced the 16S ribosomal RNA gene that is present in bacterial species. As the cost of sequencing has fallen, though, metagenomics experiments have increasingly used unbiased shotgun sequencing to capture all the organisms in a sample. This approach requires a method for estimating abundance directly from the raw read data. Here we describe a fast, accurate new method that computes the abundance at the species level using the reads collected in a metagenomics experiment. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN) uses the taxonomic assignments made by Kraken, a very fast read-level classifier, along with information about the genomes themselves to estimate abundance at the species level, the genus level, or above. We demonstrate that Bracken can produce accurate species- and genus-level abundance estimates even when a sample contains multiple near-identical species.
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Author Contributions Jennifer Lu and Florian P. Breitwieser conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, performed the computation work, reviewed drafts of the paper.Peter Thielen performed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.Steven L. Salzberg conceived and designed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.
ISSN:2376-5992
2376-5992
DOI:10.7717/peerj-cs.104