TY - JOUR UR - https://doi.org/10.7717/peerj-cs.104 DO - 10.7717/peerj-cs.104 TI - Bracken: estimating species abundance in metagenomics data AU - Lu,Jennifer AU - Breitwieser,Florian P. AU - Thielen,Peter AU - Salzberg,Steven L. A2 - Procter,James DA - 2017/01/02 PY - 2017 KW - Metagenomics KW - Species abundance KW - Microbiome KW - Bayesian estimation AB - 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. VL - 3 SP - e104 T2 - PeerJ Computer Science JO - PeerJ Computer Science J2 - PeerJ Computer Science SN - 2376-5992 ER -