robust computational analysis of rrna hypervariable tag datasets强劲的计算分析rrna超变量标签数据集.pdfVIP

Robust Computational Analysis of rRNA Hypervariable Tag Datasets 1,2 1,2 1,2 1 4 5 Maksim Sipos , Patricio Jeraldo , Nicholas Chia , Ani Qu , A. Singh Dhillon , Michael E. Konkel , Karen E. Nelson6, Bryan A. White1,3, Nigel Goldenfeld 1,2* 1 Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America, 2 Loomis Laboratory of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America, 3 Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America, 4 Avian Health and Food Safety Laboratory, Washington State University, Puyallup, Washington, United States of America, 5 School of Molecular Biosciences, Washington State University, Pullman, Washington, United States of America, 6 The J. Craig Venter Institute, Rockville, Maryland, United States of America Abstract Next-generation DNA sequencing is increasingly being utilized to probe microbial communities, such as gastrointestinal microbiomes, where it is important to be able to quantify measures of abundance and diversity. The fragmented nature of the 16S rRNA datasets obtained, coupled with their unprecedented size, has led to the recognition that the results of such analyses are potentially contaminated by a variety of artifacts, both experimental and computational. Here we quantify how multiple alignment and clustering errors contribute to overestimates of abundance and diversity, reflected by incorrect OTU assignment, corrupted phylogenies, inaccurate species diversity estimators, and rank abundance distribution functions. We show that straightforward procedural optimizations, combining preexisting tools,