QIIME 2 Enables Comprehensive End‐to‐End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data

Current Protocols in Bioinformatics - Tập 70 Số 1 - 2020
Mehrbod Estaki1,2, Lingjing Jiang3,2, Nicholas A. Bokulich4,5, Daniel McDonald1, Antonio González1, Tomasz Kościółek1,6, Cameron Martino7,8, Qiyun Zhu1, Amanda Birmingham9, Yoshiki Vázquez‐Baeza8,10, Matthew R. Dillon4, Evan Bolyen4, J. Gregory Caporaso4,5, Rob Knight8,11,12,1
1Department of Pediatrics, University of California San Diego, La Jolla, California
2Mehrbod Estaki and Lingjing Jiang should be regarded as joint first authors
3Division of Biostatistics, University of California San Diego, La Jolla, California
4Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona
5Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona.
6Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
7Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, California
8Center for Microbiome Innovation, University of California San Diego, La Jolla, California
9Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, California
10Jacobs School of Engineering, University of California San Diego, La Jolla, California
11Department of Bioengineering, University of California San Diego, La Jolla, California
12Department of Computer Science and Engineering, University of California San Diego, La Jolla, California

Tóm tắt

AbstractQIIME 2 is a completely re‐engineered microbiome bioinformatics platform based on the popular QIIME platform, which it has replaced. QIIME 2 facilitates comprehensive and fully reproducible microbiome data science, improving accessibility to diverse users by adding multiple user interfaces. QIIME 2 can be combined with Qiita, an open‐source web‐based platform, to re‐use available data for meta‐analysis. The following basic protocol describes how to install QIIME 2 on a single computer and analyze microbiome sequence data, from processing of raw DNA sequence reads through generating publishable interactive figures. These interactive figures allow readers of a study to interact with data with the same ease as its authors, advancing microbiome science transparency and reproducibility. We also show how plug‐ins developed by the community to add analysis capabilities can be installed and used with QIIME 2, enhancing various aspects of microbiome analyses—e.g., improving taxonomic classification accuracy. Finally, we illustrate how users can perform meta‐analyses combining different datasets using readily available public data through Qiita. In this tutorial, we analyze a subset of the Early Childhood Antibiotics and the Microbiome (ECAM) study, which tracked the microbiome composition and development of 43 infants in the United States from birth to 2 years of age, identifying microbiome associations with antibiotic exposure, delivery mode, and diet. For more information about QIIME 2, see https://qiime2.org. To troubleshoot or ask questions about QIIME 2 and microbiome analysis, join the active community at https://forum.qiime2.org. © 2020 The Authors.Basic Protocol: Using QIIME 2 with microbiome dataSupport Protocol: Further microbiome analyses

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Current Protocols in Bioinformatics

Tập 70 Số 1

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