Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Open accessAbstract
QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and 1565057 to R.K. Partial support was also provided by the following: grants NIH U54CA143925 (J.G.C. and T.P.) and U54MD012388 (J.G.C. and T.P.); grants from the Alfred P. Sloan Foundation (J.G.C. and R.K.); ERCSTG project MetaPG (N.S.); the Strategic Priority Research Program of the Chinese Academy of Sciences QYZDB-SSW-SMC021 (Y.B.); the Australian National Health and Medical Research Council APP1085372 (G.A.H., J.G.C., Von Bing Yap and R.K.); the Natural Sciences and Engineering Research Council (NSERC) to D.L.G.; and the State of Arizona Technology and Research Initiative Fund (TRIF), administered by the Arizona Board of Regents, through Northern Arizona University. All NCI coauthors were supported by the Intramural Research Program of the National Cancer Institute. S.M.G. and C. Diener were supported by the Washington Research Foundation Distinguished Investigator Award.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
The citation lists haven’t been fetched yet
References 29 · Cited by 23,742
Research works printed but not linked: 1
- [16]Bokulich N J. Open Source Softw 3, 934 (2018).
- Authors
- Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J. E., Bittinger, K., Brejnrod, A., Brislawn, C. J., Brown, C. T., Callahan, B. J., Caraballo-Rodríguez, A. M., Chase, J., Cope, E. K., Da Silva, R., Diener, C., Dorrestein, P. C., Douglas, G. M., Durall, D. M., Duvallet, C., Edwardson, C. F., Ernst, M., Estaki, M., Fouquier, J., Gauglitz, J. M., Gibbons, S. M., Gibson, D. L., Gonzalez, A., Gorlick, K., Guo, J., Hillmann, B., Holmes, S., Holste, H., Huttenhower, C., Huttley, G. A., Janssen, S., Jarmusch, A. K., Jiang, L., Kaehler, B. D., Kang, K. B., Keefe, C. R., Keim, P., Kelley, S. T., Knights, D., Koester, I., Kosciolek, T., Kreps, J., Langille, M. G. I., Lee, J., Ley, R., Liu, Y.-X., Loftfield, E., Lozupone, C., Maher, M., Marotz, C., Martin, B. D., McDonald, D., McIver, L. J., Melnik, A. V., Metcalf, J. L., Morgan, S. C., Morton, J. T., Naimey, A. T., Navas-Molina, J. A., Nothias, L. F., Orchanian, S. B., Pearson, T., Peoples, S. L., Petras, D., Preuss, M. L., Pruesse, E., Rasmussen, L. B., Rivers, A., Robeson, M. S., Rosenthal, P., Segata, N., Shaffer, M., Shiffer, A., Sinha, R., Song, S. J., Spear, J. R., Swafford, A. D., Thompson, L. R., Torres, P. J., Trinh, P., Tripathi, A., Turnbaugh, P. J., Ul-Hasan, S., van der Hooft, J. J. J., Vargas, F., Vázquez-Baeza, Y., Vogtmann, E., von Hippel, M., Walters, W., Wan, Y., Wang, M., Warren, J., Weber, K. C., Williamson, C. H. D., Willis, A. D., Xu, Z. Z., Zaneveld, J. R., Zhang, Y., Zhu, Q., Knight, R., & Caporaso, J. G.
- Affiliations
- Northern Arizona University (US)
- National Cancer Institute (US)
- Woods Hole Oceanographic Institution (US)
- Massachusetts Institute of Technology (US)
- University of Copenhagen (DK)
- University of Trento (IT)
- Chinese Academy of Sciences (CN)
- University of California, San Francisco (US)
- Children's Hospital of Philadelphia (US)
- Pacific Northwest National Laboratory (US)
- University of California, Davis (US)
- North Carolina State University (US)
- Institute for Systems Biology (US)
- University of California San Diego (US)
- Dalhousie University (CA)
- University of British Columbia (CA)
- Shedd Aquarium (US)
- Statens Serum Institut (DK)
- University of British Columbia, Okanagan Campus (CA)
- University of Colorado Anschutz (US)
- University of Washington (US)
- Michigan State University (US)
- University of Minnesota (US)
- Stanford University (US)
- Broad Institute (US)
- Australian National University (AU)
- Heinrich Heine University Düsseldorf (DE)
- Sookmyung Women's University (KR)
- San Diego State University (US)
- Scripps Institution of Oceanography (US)
- Howard Hughes Medical Institute (US)
- Cornell University (US)
- Colorado State University (US)
- Google (United States) (US)
- University of Washington Bothell (US)
- Webster University (US)
- Agricultural Research Service (US)
- University of Arkansas for Medical Sciences (US)
- Colorado School of Mines (US)
- National Oceanic and Atmospheric Administration (US)
- University of California, Merced (US)
- Max Planck Institute for Developmental Biology (DE)
- Environment Agency (GB)
- Merck & Co., Inc., Rahway, NJ, USA (United States) (US)
- Corresponding author
- Caporaso, J. Gregory
- ORCID
- Bolyen, Evan
- Rideout, Jai Ram
- Dillon, Matthew R.
- Bokulich, Nicholas A.
- Abnet, Christian C.
- Al-Ghalith, Gabriel A.
- Alexander, Harriet
- Alm, Eric J.
- Arumugam, Manimozhiyan
- Asnicar, Francesco
- Bai, Yang
- Bisanz, Jordan E.
- Bittinger, Kyle
- Brejnrod, Asker
- Brislawn, Colin J.
- Brown, C. Titus
- Callahan, Benjamin J.
- Caraballo-Rodríguez, Andrés Mauricio
- Cope, Emily K.
- Diener, Christian
- Dorrestein, Pieter C.
- Douglas, Gavin M.
- Durall, Daniel M.
- Duvallet, Claire
- Edwardson, Christian F.
- Ernst, Madeleine
- Estaki, Mehrbod
- Fouquier, Jennifer
- Gauglitz, Julia M.
- Gibbons, Sean M.
- Gibson, Deanna L.
- Guo, Jiarong
- Hillmann, Benjamin
- Holmes, Susan
- Holste, Hannes
- Huttenhower, Curtis
- Huttley, Gavin A.
- Janssen, Stefan
- Jarmusch, Alan K.
- Jiang, Lingjing
- Kaehler, Benjamin D.
- Kang, Kyo Bin
- Keefe, Christopher R.
- Keim, Paul
- Kelley, Scott T.
- Knights, Dan
- Koester, Irina
- Kosciolek, Tomasz
- Kreps, Jorden
- Langille, Morgan G. I.
- Lee, Joslynn
- Ley, Ruth
- Liu, Yong-Xin
- Loftfield, Erikka
- Lozupone, Catherine
- Marotz, Clarisse
- Martin, Bryan D.
- McDonald, Daniel
- McIver, Lauren J.
- Melnik, Alexey V.
- Metcalf, Jessica L.
- Morgan, Sydney C.
- Navas-Molina, Jose A.
- Orchanian, Stephanie B.
- Pearson, Talima
- Petras, Daniel
- Pruesse, Elmar
- Rivers, Adam
- Robeson, Michael S.
- Segata, Nicola
- Sinha, Rashmi
- Song, Se Jin
- Spear, John R.
- Swafford, Austin D.
- Thompson, Luke R.
- Torres, Pedro J.
- Tripathi, Anupriya
- Turnbaugh, Peter J.
- Ul-Hasan, Sabah
- van der Hooft, Justin J. J.
- Vargas, Fernando
- Vogtmann, Emily
- von Hippel, Max
- Walters, William
- Wan, Yunhu
- Wang, Mingxun
- Warren, Jonathan
- Weber, Kyle C.
- Willis, Amy D.
- Xu, Zhenjiang Zech
- Zaneveld, Jesse R.
- Zhang, Yilong
- Zhu, Qiyun
- Knight, Rob
- Caporaso, J. Gregory
- Venue
- Nature Biotechnology
- Published
- 2019-07-24
- Volume
- 37
- Issue
- 8
- Pages
- 852-857
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC7015180
- OpenAlex
- W2963276645
- Semantic Scholar
- 133bcd7488a3c07cb0f493a87564c30e5433768c
- Cited by
- 23,742
- References
- 29
- Citations by year
- 2026: 3681 · 2025: 4408 · 2024: 4419 · 2023: 3650 · 2022: 3366 · 2021: 2697 · 2020: 1322 · 2019: 182 · 2018: 1 · 2017: 1 · 2016: 1 · 2015: 1 · 2013: 1
- FWCI
- 2256.30
- Type
- journal article
- Language
- en
- Update notices
- correction (2019-08-09)
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Biotechnology (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, other-oa)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Iris (University of Trento) (submittedVersion, other-oa)
- Aquila Digital Community (University of Southern Mississippi) (submittedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
- Institutional Research Information System (Università degli Studi di Trento) (submittedVersion)
- Socio-Environmental Systems Modeling (submittedVersion)
- NOAA Institutional Repository (submittedVersion, public-domain)
- ANU Open Research (Australian National University) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Funders
- National Science Foundation (1565100, 1565057)
- U.S. Department of Agriculture
- Alfred P. Sloan Foundation
- Washington Research Foundation
- Massachusetts Institute of Technology
- San Diego State University
- Florida Atlantic University
- Northern Arizona University (U54MD012388)
- Arizona Board of Regents
- Universidad del Atlántico
- Chinese Academy of Sciences (QYZDB-SSW-SMC021)
- Karolinska Institutet
- Max-Planck-Gesellschaft
- Tianjin University
- Universitetet i Bergen
- Karl-Franzens-Universität Graz
- Stockholms Universitet
- Medizinische Universität Graz
- Haukeland Universitetssjukehus
- National Institutes of Health (Z99 CA999999, 10,11)
- Agricultural Research Service
- Natural Sciences and Engineering Research Council of Canada
- Medical Research Council
- National Health and Medical Research Council (1085372)
- National Cancer Institute (U54CA143925)
- National Institute of General Medical Sciences (R35GM133420)
- National Institute of Environmental Health Sciences (T32ES015459)
- National Institute on Minority Health and Health Disparities (U54MD012388)
- Topics
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- QIIME2, reproducibility, interactive data analysis, scalability, extensibility, bioinformatics software
- MeSH terms
- Data Science, Humans, Software, Databases, Factual, Computational Biology, Microbiota
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
