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

Justin Kuczynski, Jesse Stombaugh, William Anton Walters, Antonio González, J. Gregory Caporaso, Rob Knight

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
JournalCurrent Protocols in Bioinformatics
VolumeChapter 10
StatePublished - Dec 2011
Externally publishedYes

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Nucleic acid sequences
Ecology
rRNA Genes
Application programs
Nucleic Acids
Software
Genes
Network protocols

ASJC Scopus subject areas

  • Medicine(all)

Cite this

Kuczynski, J., Stombaugh, J., Walters, W. A., González, A., Caporaso, J. G., & Knight, R. (2011). Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Current Protocols in Bioinformatics, Chapter 10.

Using QIIME to analyze 16S rRNA gene sequences from microbial communities. / Kuczynski, Justin; Stombaugh, Jesse; Walters, William Anton; González, Antonio; Caporaso, J. Gregory; Knight, Rob.

In: Current Protocols in Bioinformatics, Vol. Chapter 10, 12.2011.

Research output: Contribution to journalArticle

Kuczynski, J, Stombaugh, J, Walters, WA, González, A, Caporaso, JG & Knight, R 2011, 'Using QIIME to analyze 16S rRNA gene sequences from microbial communities.', Current Protocols in Bioinformatics, vol. Chapter 10.
Kuczynski J, Stombaugh J, Walters WA, González A, Caporaso JG, Knight R. Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Current Protocols in Bioinformatics. 2011 Dec;Chapter 10.
Kuczynski, Justin ; Stombaugh, Jesse ; Walters, William Anton ; González, Antonio ; Caporaso, J. Gregory ; Knight, Rob. / Using QIIME to analyze 16S rRNA gene sequences from microbial communities. In: Current Protocols in Bioinformatics. 2011 ; Vol. Chapter 10.
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