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      QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

      Preprint

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          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.

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          Most cited references 1

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          DADA2: High resolution sample inference from Illumina amplicon data

          We present DADA2, a software package that models and corrects Illumina-sequenced amplicon errors. DADA2 infers sample sequences exactly, without coarse-graining into OTUs, and resolves differences of as little as one nucleotide. In several mock communities DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.
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            Author and article information

            Journal
            PeerJ
            October 24 2018
            Affiliations
            [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 Population Health and Reproduction, University of California, Davis, CA, USA
            [6 ]Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
            [7 ]Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
            [8 ]University of Copenhagen, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, Copenhagen, Denmark
            [9 ]Centre for Integrative Biology, University of Trento, Trento, Italy
            [10 ]State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
            [11 ]Centre of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences & John Innes Centre, Beijing, China
            [12 ]University of Chinese Academy of Sciences, Beijing, China
            [13 ]Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
            [14 ]Division of Gastroenterology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
            [15 ]Hepatology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
            [16 ]Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
            [17 ]Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
            [18 ]Department of Population Health & Pathobiology, North Carolina State University, Raleigh, NC, USA
            [19 ]Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
            [20 ]Collaborative mass spectrometry innovation center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
            [21 ]Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
            [22 ]Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
            [23 ]Irving K. Barber School of Arts and Sciences, University of British Columbia, Kelowna, British Columbia, Canada
            [24 ]A. Watson Armour III Center for Animal Health and Welfare, Aquarium Microbiome Project, John G. Shedd Aquarium, Chicago, IL, USA
            [25 ]Department of Biology, University of British Columbia Okanagan, Okanagan, BC, Canada
            [26 ]Computational Bioscience Graduate Program, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, USA
            [27 ]Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, USA
            [28 ]Irving K. Barber School of Arts and Sciences, Department of Biology, The University of British Columbia, Kelowna, BC, Canada
            [29 ]Department of Medicine, The University of British Columbia, Kelowna, BC, Canada
            [30 ]Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
            [31 ]Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
            [32 ]Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
            [33 ]Stanford University, Statistics Department, Palo Alto, CA, USA
            [34 ]Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
            [35 ]Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
            [36 ]Broad Institute of MIT and Harvard, Cambridge, MA, USA
            [37 ]Research School of Biology, The Australian National University, Canberra, ACT, Australia
            [38 ]Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Dusseldorf, Germany
            [39 ]Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
            [40 ]College of Pharmacy, Sookmyung Women's University, Seoul, Republic of Korea
            [41 ]San Diego State University, Department of Biology, San Diego, CA, USA
            [42 ]Biotechnology Institute, University of Minnesota, Saint Paul, MN, USA
            [43 ]Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
            [44 ]Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
            [45 ]Science Education, Howard Hughes Medical Institute, Ashburn, VA, USA
            [46 ]Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
            [47 ]Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
            [48 ]Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Denver Anschutz Medical Campus, Aurona, CO, USA
            [49 ]Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA
            [50 ]Department of Statistics, University of Washington, Seattle, WA, USA
            [51 ]Department of Animal Science, Colorado State University, Fort Collins, CO, USA
            [52 ]Irving K. Barber School of Arts and Sciences, Unit 2 (Biology), University of British Columbia, Kelowna, BC, Canada
            [53 ]Mountain View, Google LLC, Mountain View, CA, USA
            [54 ]Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
            [55 ]School of Information Studies, Syracuse University, Syracuse, NY, USA
            [56 ]School of STEM, University of Washington Bothell, Bothell, WA, USA
            [57 ]Department of Biological Sciences, Webster University, St Louis, MO, USA
            [58 ]Agricultural Research Service, Genomics and Bioinformatics Research Unit, United States Department of Agriculture, Gainesville, FL, USA
            [59 ]College of Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
            [60 ]Computational Bioscience Program, University of Colorado Denver Anschutz Medical Campus, Aurona, CO, USA
            [61 ]Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA
            [62 ]Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, Mississippi, USA
            [63 ]Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
            [64 ]Department of Biology, San Diego State University, San Diego, CA, USA
            [65 ]Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
            [66 ]Division of Biological Sciences, University of California San Diego, San Diego, CA, USA
            [67 ]Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
            [68 ]Quantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA, USA
            [69 ]Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
            [70 ]Department of Mathematics, University of Arizona, Tucson, AZ, USA
            [71 ]National Laboratory Service, Environment Agency, Starcross, UK
            [72 ]College of Agriculture and Life Sciences, University of Florida, Gainesville, FL, USA
            [73 ]Department of Biostatistics, University of Washington, Seattle, WA, USA
            [74 ]University of Washington Bothell, School of STEM, Division of Biological Sciences, Bothell, WA, USA
            [75 ]Merck & Co. Inc., Kenilworth, NJ, USA
            [76 ]Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
            Article
            10.7287/peerj.preprints.27295v1
            © 2018

            http://creativecommons.org/licenses/by/4.0/

            Product
            Self URI (article page): https://peerj.com/preprints/27295

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