Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities

Justin Kuczynski1, Jesse Stombaugh2, William Anton Walters1, Antonio González3, J. Gregory Caporaso4, Rob Knight2

1 Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, 2 Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, 3 Department of Computer Science, University of Colorado, Boulder, Colorado, 4 Department of Computer Science, Northern Arizona University, Flagstaff, Arizona
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 10.7
DOI:  10.1002/0471250953.bi1007s36
Online Posting Date:  December, 2011
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Abstract

QIIME (canonically pronounced “chime”) is a software application that performs microbial community analysis. It is an acronym for Quantitative Insights Into Microbial Ecology, and has been used to analyze and interpret nucleic acid sequence data from fungal, viral, bacterial, and archaeal communities. The following protocols describe how to install QIIME on a single computer and use it to analyze microbial 16S sequence data from nine distinct microbial communities. Curr. Protoc. Bioinform. 36:10.7.1‐10.7.20. © 2011 by John Wiley & Sons, Inc.

Keywords: microbial ecology; 16S; SSU; software; bioinformatics; QIIME

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Acquiring an Example Study and Demultiplexing DNA Sequences
  • Basic Protocol 2: Picking OTUs, Assigning Toxonomy, Inferring Phylogeny, and Creating an OTU Table
  • Basic Protocol 3: Alpha Diversity within Samples and Rarefaction Curves
  • Basic Protocol 4: Beta Diversity Between Samples and Beta Diversity Plots
  • Support Protocol 1: Installing QIIME via VirtualBox
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Literature Cited

Literature Cited
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