Using QIIME to analyze 16S rRNA gene sequences from microbial communities

Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 12/2011; Chapter 10:Unit 10.7.. DOI: 10.1002/0471250953.bi1007s36
Source: PubMed

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.

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Available from: William A Walters, Nov 03, 2014
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    • "quencing was performed , follow - ing an additional amplification step using the 27F - 519R primer pair for the 16S rRNA amplicon sequences on an Illumina MiSeq ( at Molecular Research LP ; Shallowater , TX , USA ) following the manufacturer ' s guidelines . 16S rRNA gene sequences were analyzed using the QIIME pipeline ( Caporaso et al . , 2010 ; Kuczynski et al . , 2011 ) . De novo Operational Taxonomic Units ( OTUs ) were defined at 97% sequence identity using UCLUST ( Edgar , 2010 ) and taxonomy was assigned to the Greengenes database ( version"
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