Bracken: estimating species abundance in metagenomics data

Author:

Lu Jennifer12,Breitwieser Florian P.2,Thielen Peter3,Salzberg Steven L.124

Affiliation:

1. Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States

2. Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States

3. Applied Physics Laboratory, Johns Hopkins University, Laurel, MD, United States

4. Departments of Computer Science and Biostatistics, Johns Hopkins University, Baltimore, MD, United States

Abstract

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.

Funder

US National Institutes of Health

US Army Research Office

Publisher

PeerJ

Subject

General Computer Science

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