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

Evan Bolyen¹, Jai Ram Rideout¹, Matthew R Dillon¹, Nicholas A Bokulich¹, Christian C Abnet², Gabriel A Al-Ghalith³, Harriet Alexander^{4

5}, Eric J Alm^{6

7}, Manimozhiyan Arumugam⁸, Francesco Asnicar⁹, Yang Bai^{10

11

12}, Jordan E Bisanz¹³, Kyle Bittinger^{14

15}, Asker Brejnrod⁸, Colin J Brislawn¹⁶, C Titus Brown⁵, Benjamin J Callahan^{17

18}, Andrés Mauricio Caraballo-Rodríguez¹⁹, John Chase¹, Emily K Cope^{1

20}, Ricardo Da Silva¹⁹, Christian Diener²¹, Pieter C Dorrestein¹⁹, Gavin M Douglas²², Daniel M Durall²³, Claire Duvallet⁶, Christian F Edwardson²⁴, Madeleine Ernst^{19

25}, Mehrbod Estaki²⁶, Jennifer Fouquier^{27

28}, Julia M Gauglitz¹⁹, Sean M Gibbons^{21

29}, Deanna L Gibson^{30

31}, Antonio Gonzalez³², Kestrel Gorlick¹, Jiarong Guo³³, Benjamin Hillmann³, Susan Holmes³⁴, Hannes Holste^{32

35}, Curtis Huttenhower^{36

37}, Gavin A Huttley³⁸, Stefan Janssen³⁹, Alan K Jarmusch¹⁹, Lingjing Jiang⁴⁰, Benjamin D Kaehler^{38

41}, Kyo Bin Kang^{19

42}, Christopher R Keefe¹, Paul Keim¹, Scott T Kelley⁴³, Dan Knights^{3

44}, Irina Koester^{19

45}, Tomasz Kosciolek⁴⁶, Jorden Kreps¹, Morgan G I Langille⁴⁷, Joslynn Lee⁴⁸, Ruth Ley^{49

50}, Yong-Xin Liu^{10

11}, Erikka Loftfield², Catherine Lozupone²⁸, Massoud Maher⁵¹, Clarisse Marotz³², Bryan D Martin⁵², Daniel McDonald³², Lauren J McIver^{36

37}, Alexey V Melnik¹⁹, Jessica L Metcalf⁵³, Sydney C Morgan⁵⁴, Jamie T Morton^{32

51}, Ahmad Turan Naimey¹, Jose A Navas-Molina^{32

51

55}, Louis Felix Nothias¹⁹, Stephanie B Orchanian⁵⁶, Talima Pearson¹, Samuel L Peoples^{57

58}, Daniel Petras¹⁹, Mary Lai Preuss⁵⁹, Elmar Pruesse²⁸, Lasse Buur Rasmussen⁸, Adam Rivers⁶⁰, Michael S Robeson 2nd⁶¹, Patrick Rosenthal⁵⁹, Nicola Segata⁹, Michael Shaffer^{27

28}, Arron Shiffer¹, Rashmi Sinha², Se Jin Song³², John R Spear⁶², Austin D Swafford⁵⁶, Luke R Thompson^{63

64}, Pedro J Torres⁴³, Pauline Trinh⁶⁵, Anupriya Tripathi^{19

32

66}, Peter J Turnbaugh⁶⁷, Sabah Ul-Hasan⁶⁸, Justin J J van der Hooft⁶⁹, Fernando Vargas⁶⁶, Yoshiki Vázquez-Baeza³², Emily Vogtmann², Max von Hippel⁷⁰, William Walters⁴⁹, Yunhu Wan², Mingxun Wang¹⁹, Jonathan Warren⁷¹, Kyle C Weber^{60

72}, Charles H D Williamson⁷³, Amy D Willis⁷⁴, Zhenjiang Zech Xu³², Jesse R Zaneveld⁷⁵, Yilong Zhang⁷⁶, Qiyun Zhu³², Rob Knight^{32

56

35}, J Gregory Caporaso^{77

78}

Affiliations

¹ Center for Applied Microbiome Science, 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, MN, USA.
⁴ Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
⁵ Department of Population Health and Reproduction, University of California, Davis, 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 Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 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, 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 Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
¹⁷ Department of Population Health & Pathobiology, North Carolina State University, Raleigh, NC, USA.
¹⁸ Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.
¹⁹ Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
²⁰ Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
²¹ Institute for Systems Biology, Seattle, WA, 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 Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark.
²⁶ Department of Biology, University of British Columbia Okanagan, Okanagan, British Columbia, Canada.
²⁷ Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
²⁸ Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
²⁹ eScience Institute, University of Washington, Seattle, WA, USA.
³⁰ Irving K. Barber School of Arts and Sciences, Department of Biology, University of British Columbia, Kelowna, British Columbia, Canada.
³¹ Department of Medicine, University of British Columbia, Kelowna, British Columbia, Canada.
³² Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
³³ Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA.
³⁴ Statistics Department, Stanford University, Palo Alto, CA, USA.
³⁵ Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
³⁶ Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
³⁷ Broad Institute of MIT and Harvard, Cambridge, MA, USA.
³⁸ Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.
³⁹ Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Dusseldorf, Germany.
⁴⁰ Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA.
⁴¹ School of Science, University of New South Wales, Canberra, Australian Capital Territory, Australia.
⁴² College of Pharmacy, Sookmyung Women's University, Seoul, Republic of Korea.
⁴³ Department of Biology, San Diego State University, San Diego, CA, USA.
⁴⁴ Biotechnology Institute, University of Minnesota, Saint Paul, MN, USA.
⁴⁵ Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
⁴⁶ Department of Pediatrics, University of California San Diego, La Jolla, California, USA.
⁴⁷ Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada.
⁴⁸ Science Education, Howard Hughes Medical Institute, Ashburn, VA, USA.
⁴⁹ Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany.
⁵⁰ Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
⁵¹ Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA.
⁵² Department of Statistics, University of Washington, Seattle, WA, USA.
⁵³ Department of Animal Science, Colorado State University, Fort Collins, CO, USA.
⁵⁴ Irving K. Barber School of Arts and Sciences, Unit 2 (Biology), University of British Columbia, Kelowna, British Columbia, Canada.
⁵⁵ Google LLC, Mountain View, CA, USA.
⁵⁶ Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
⁵⁷ School of Information Studies, Syracuse University, Syracuse, NY, USA.
⁵⁸ School of STEM, University of Washington Bothell, Bothell, WA, USA.
⁵⁹ Department of Biological Sciences, Webster University, St. Louis, MO, USA.
⁶⁰ Agricultural Research Service, Genomics and Bioinformatics Research Unit, United States Department of Agriculture, Gainesville, FL, USA.
⁶¹ College of Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
⁶² Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA.
⁶³ Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, MS, USA.
⁶⁴ Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, La Jolla, 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 Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
⁷⁴ Department of Biostatistics, University of Washington, Seattle, WA, USA.
⁷⁵ School of STEM, Division of Biological Sciences, University of Washington Bothell, Bothell, WA, USA.
⁷⁶ Merck & Co. Inc., Kenilworth, NJ, USA.
⁷⁷ Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA. greg.caporaso@nau.edu.
⁷⁸ Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA. greg.caporaso@nau.edu.

PMID: 31341288
PMCID: PMC7015180
DOI: 10.1038/s41587-019-0209-9

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

Evan Bolyen et al. Nat Biotechnol. 2019 Aug.

. 2019 Aug;37(8):852-857.

doi: 10.1038/s41587-019-0209-9.

Authors

Affiliations

¹ Center for Applied Microbiome Science, 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, MN, USA.
⁴ Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
⁵ Department of Population Health and Reproduction, University of California, Davis, 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 Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 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, 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 Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
¹⁷ Department of Population Health & Pathobiology, North Carolina State University, Raleigh, NC, USA.
¹⁸ Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.
¹⁹ Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
²⁰ Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
²¹ Institute for Systems Biology, Seattle, WA, 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 Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark.
²⁶ Department of Biology, University of British Columbia Okanagan, Okanagan, British Columbia, Canada.
²⁷ Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
²⁸ Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
²⁹ eScience Institute, University of Washington, Seattle, WA, USA.
³⁰ Irving K. Barber School of Arts and Sciences, Department of Biology, University of British Columbia, Kelowna, British Columbia, Canada.
³¹ Department of Medicine, University of British Columbia, Kelowna, British Columbia, Canada.
³² Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
³³ Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA.
³⁴ Statistics Department, Stanford University, Palo Alto, CA, USA.
³⁵ Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
³⁶ Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
³⁷ Broad Institute of MIT and Harvard, Cambridge, MA, USA.
³⁸ Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.
³⁹ Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Dusseldorf, Germany.
⁴⁰ Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA.
⁴¹ School of Science, University of New South Wales, Canberra, Australian Capital Territory, Australia.
⁴² College of Pharmacy, Sookmyung Women's University, Seoul, Republic of Korea.
⁴³ Department of Biology, San Diego State University, San Diego, CA, USA.
⁴⁴ Biotechnology Institute, University of Minnesota, Saint Paul, MN, USA.
⁴⁵ Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
⁴⁶ Department of Pediatrics, University of California San Diego, La Jolla, California, USA.
⁴⁷ Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada.
⁴⁸ Science Education, Howard Hughes Medical Institute, Ashburn, VA, USA.
⁴⁹ Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany.
⁵⁰ Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
⁵¹ Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA.
⁵² Department of Statistics, University of Washington, Seattle, WA, USA.
⁵³ Department of Animal Science, Colorado State University, Fort Collins, CO, USA.
⁵⁴ Irving K. Barber School of Arts and Sciences, Unit 2 (Biology), University of British Columbia, Kelowna, British Columbia, Canada.
⁵⁵ Google LLC, Mountain View, CA, USA.
⁵⁶ Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
⁵⁷ School of Information Studies, Syracuse University, Syracuse, NY, USA.
⁵⁸ School of STEM, University of Washington Bothell, Bothell, WA, USA.
⁵⁹ Department of Biological Sciences, Webster University, St. Louis, MO, USA.
⁶⁰ Agricultural Research Service, Genomics and Bioinformatics Research Unit, United States Department of Agriculture, Gainesville, FL, USA.
⁶¹ College of Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
⁶² Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA.
⁶³ Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, MS, USA.
⁶⁴ Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, La Jolla, 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 Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
⁷⁴ Department of Biostatistics, University of Washington, Seattle, WA, USA.
⁷⁵ School of STEM, Division of Biological Sciences, University of Washington Bothell, Bothell, WA, USA.
⁷⁶ Merck & Co. Inc., Kenilworth, NJ, USA.
⁷⁷ Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA. greg.caporaso@nau.edu.
⁷⁸ Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA. greg.caporaso@nau.edu.

PMID: 31341288
PMCID: PMC7015180
DOI: 10.1038/s41587-019-0209-9

Erratum in

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson … See abstract for full author list ➔ Bolyen E, et al. Nat Biotechnol. 2019 Sep;37(9):1091. doi: 10.1038/s41587-019-0252-6. Nat Biotechnol. 2019. PMID: 31399723

No abstract available

PubMed Disclaimer

Figures

**Fig. 1 |. QIIME 2 provides many interactive visualization tools.**
The products of four worked examples are presented here, and interactive versions of these screen captures are available in Supplementary File 1 and at https://github.com/qiime2/paper1. Detailed descriptions and methods, including the commands used to generate each of these visualizations, are provided in Supplementary Methods. a, Unweighted UniFrac principal coordinate analysis plot containing 37,680 samples, illustrating the scalability of QIIME 2. Colors indicate sample type, as described by the Earth Microbiome Project ontology (EMPO). b, Interactive taxonomic composition bar plot illustrating the phylum-level composition of microbial-mat samples collected along a temperature gradient in Yellowstone National Park Hot Spring outflow channels (Steep Cone Geyser). The many interactive controls available in this plot vastly decrease the burden of exploratory analysis over QIIME 1. c, Feature volatility plot (https://msystems.asm.org/content/3/6/e00219-18) illustrating the change in *Bifidobacterium* abundance over time in breast-fed and formula-fed infants. Temporally interesting features can be interactively discovered with this visualization. Bar charts rank the importance (predictive power for time point) and mean abundance of all microbial features. These bar charts provide an interface for visualizing volatility plots (line plots) of individual features in the context of their importance and abundance; clicking on a bar will display the volatility plot of that feature and highlight in blue that feature’s importance and abundance in the bar charts below. d, Molecular cartography of the human skin surface. Colored spots represent the abundance of the small-molecule cosmetic ingredient sodium laureth sulfate on the human skin. Sample data can be interactively visualized in three-dimensional models, thus supporting the discovery of spatial patterns.

**Fig. 2 |. QIIME 2 iteratively records data provenance, ensuring bioinformatics reproducibility.**
This simplified diagram illustrates the automatically tracked information regarding the creation of the taxonomy bar plot presented in Fig. 1b. QIIME 2 results (circles) contain network diagrams illustrating the data provenance stored in the result. Actions (quadrilaterals) are applied to QIIME 2 results and generate new results. Arrows indicate the flow of QIIME 2 results through actions. TaxonomicClassifier and FeatureData[Sequence] inputs contain independent provenance (red and blue, respectively) and are provided to a classify action (yellow), which taxonomically annotates sequences. The result of the classify action, a FeatureData[Taxonomy] result, integrates the provenance of both inputs with the classify action. This result is then provided to the barplot action with a FeatureTable[Frequency] input, which shares some provenance with the FeatureData[Sequence] input, because they were generated from the same upstream analysis. The resulting visualization (Fig. 1b) has the complete data provenance and correctly identifies shared processing of inputs. This simplified representation was created manually from the complete provenance graph for the purpose of illustration. An interactive and complete version of this provenance graph (as well as those for other Fig. 1 panels) can be accessed through Supplementary File 1.

See this image and copyright information in PMC

References

1. Smith MI et al. Science 339, 548–554 (2013). - PMC - PubMed
1. Gopalakrishnan V et al. Science 359, 97–103 (2018). - PMC - PubMed
1. Gehring CA, Sthultz CM, Flores-Rentería L, Whipple AV & Whitham TG Proc. Natl Acad. Sci. USA 114, 11169–11174 (2017). - PMC - PubMed
1. Lee K, Pletcher SD, Lynch SV, Goldberg AN & Cope EK Front. Cell. Infect. Microbiol 8, 168 (2018). - PMC - PubMed
1. Metcalf JL et al. Science 351, 158–162 (2016). - PubMed

Publication types

Actions
Actions
Actions
Actions

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions

Grants and funding

LinkOut - more resources

Full Text Sources
Other Literature Sources
- Bio-protocol Exchange
- The Lens - Patent Citations Database
Medical
- ClinicalTrials.gov
Molecular Biology Databases
- NIAID Data Ecosystem - Find datasets on Infectious and Immune-mediated Diseases

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

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

Affiliations

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

Authors

Affiliations

Erratum in

Figures

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources

Medical

Molecular Biology Databases