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QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
Evan Bolyen, 1 Jai Ram Rideout, 1 Matthew R Dillon, 1 Nicholas A Bokulich, 1 Christian Abnet, 2 Gabriel A Al-Ghalith, 3 Harriet Alexander, 4 Eric J Alm, 5 Manimozhiyan Arumugam, 6 Francesco Asnicar, 7 Yang Bai, 8 Jordan E Bisanz, 9 Kyle Bittinger, 10 Asker Brejnrod, 11 Colin J Brislawn, 12 C Titus Brown, 13 Benjamin J Callahan, 14 Andrés Mauricio Caraballo-Rodríguez, 15 John Chase, 1 Emily Cope, 1 Ricardo Da Silva, 15 Pieter C Dorrestein, 15 Gavin M Douglas, 16 Daniel M Durall, 17 Claire Duvallet, 5 Christian F Edwardson, 18 Madeleine Ernst, 15 Mehrbod Estaki, 19 Jennifer Fouquier, 20 Julia M Gauglitz, 15 Deanna L Gibson, 21 Antonio Gonzalez, 22 Kestrel Gorlick, 1 Jiarong Guo, 23 Benjamin Hillmann, 24 Susan Holmes, 25 Hannes Holste, 22 Curtis Huttenhower, 26 Gavin Huttley, 27 Stefan Janssen, 28 Alan K Jarmusch, 15 Lingjing Jiang, 29 Benjamin Kaehler, 27 Kyo Bin Kang, 15 Christopher R Keefe, 1 Paul Keim, 1 Scott T Kelley, 30 Dan Knights, 31 Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan Gi Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Ii Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin Jj Van Der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max Von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase Hd Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight, J Gregory Caporaso
1  Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
2  Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA
3  Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
4  Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
5  Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
6  University of Copenhagen, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, Copenhagen, Denmark
7  Centre for Integrative Biology, University of Trento, Trento, Italy
8  State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
9  Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
10  Division of Gastroenterology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
11  Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
12  Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
13  Department of Population Health and Reproduction, University of California, Davis, CA, USA
14  Department of Population Health & Pathobiology, North Carolina State University, Raleigh, NC, USA
15  Collaborative mass spectrometry innovation center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
16  Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
17  Irving K. Barber School of Arts and Sciences, University of British Columbia, Kelowna, British Columbia, Canada
18  A. Watson Armour III Center for Animal Health and Welfare, Aquarium Microbiome Project, John G. Shedd Aquarium, Chicago, IL, USA
19  Department of Biology, University of British Columbia Okanagan, Okanagan, BC, Canada
20  Computational Bioscience Graduate Program, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, USA
21  Irving K. Barber School of Arts and Sciences, Department of Biology, The University of British Columbia, Kelowna, BC, Canada
22  Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
23  Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
24  Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
25  Stanford University, Statistics Department, Palo Alto, CA, USA
26  Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
27  Research School of Biology, The Australian National University, Canberra, ACT, Australia
28  Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
29  Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
30  San Diego State University, Department of Biology, San Diego, CA, USA
31  Department of Computer Science and Engineering, University of Minnesota, Minneapo

Published: 03 December 2018 by PeerJ
PeerJ, 10.7287/peerj.preprints.27295v2
Abstract: We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers. QIIME 2 provides new features that will drive the next generation of microbiome research. These include interactive spatial and temporal analysis and visualization tools, support for metabolomics and shotgun metagenomics analysis, and automated data provenance tracking to ensure reproducible, transparent microbiome data science.
Keywords: bioinformatics, Reproducibility, software, microbiome, microbial ecology, data science
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