Bracken: estimating species abundance in metagenomics data

TLDR

Metagenomic experiments use high‑throughput DNA sequencing to profile microbial communities, moving from phylum‑level or 16S rRNA analyses to unbiased shotgun sequencing that captures all organisms in a sample. The study aims to develop a method that estimates species‑level abundance directly from raw metagenomic reads. Bracken (Bayesian Reestimation of Abundance after Classification with Kraken) leverages Kraken’s read‑level taxonomic assignments and genome characteristics to re‑estimate abundance at species, genus, or higher levels. Bracken accurately estimates species‑ and genus‑level abundances, even in samples with closely related species.

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.