Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

TitleAccurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences
Publication TypeJournal Articles
Year of Publication2011
AuthorsLiu B, Gibbons T, Ghodsi M, Treangen T, Pop M.
JournalBMC GenomicsBMC Genomics
Volume12
Type of Article10.1186/1471-2164-12-S2-S4
ISBN Number1471-2164
Abstract

A major goal of metagenomics is to characterize the microbial composition of an environment. The most popular approach relies on 16S rRNA sequencing, however this approach can generate biased estimates due to differences in the copy number of the gene between even closely related organisms, and due to PCR artifacts. The taxonomic composition can also be determined from metagenomic shotgun sequencing data by matching individual reads against a database of reference sequences. One major limitation of prior computational methods used for this purpose is the use of a universal classification threshold for all genes at all taxonomic levels.