Qiita: rapid, web-enabled microbiome meta-analysis (original) (raw)

Data availability

All data used are available via Qiita and EBI (where applicable). The Human Microbiome Project (HMP) and iHMP data are available via the HMP Data Analysis and Coordination Center (DACC) at https://portal.hmpdacc.org/. Analytical steps for this paper can be found at https://github.com/knightlab-analyses/qiita-paper. Additionally, the Qiita analysis can be found at https://qiita.ucsd.edu/analysis/description/15093/; note that the user must log in to Qiita to access this analysis. Source data for Supplementary Fig. 1 are available online.

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Acknowledgements

We are grateful to J. Debelius, J. Jansson, D. Bazaldua, and J. Kuczynski for their help in improving Qiita via suggestion, code changes, and contributed datasets, or during the preparation of this manuscript; and to J. Gordon and his laboratory for helpful discussions. This work was supported in part by the Alfred P. Sloan Foundation (2017-9838 and 2015-13933 (R.K.)), the NIH/NIDDK (P01DK078669 (R.K.)), the NSF (DBI-1565057 and 1565100 (J.G.C. and R.K.)), the Office of Naval Research (ONR; N00014-15-1-2809 (R.K.)), and the US Army (CDMRP W81XWH-15-1-0653 (R.K.)).

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Author notes

  1. Jose A. Navas-Molina
    Present address: Google LLC, Mountain View, CA, USA
  2. Joshua Shorenstein
    Present address: Inscripta, Inc., Boulder, CO, USA
  3. These authors contributed equally: Antonio Gonzalez and Jose A. Navas-Molina.

Authors and Affiliations

  1. Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
    Antonio Gonzalez, Jose A. Navas-Molina, Tomasz Kosciolek, Daniel McDonald, Yoshiki Vázquez-Baeza, Gail Ackermann, Jeff DeReus, Stefan Janssen, Jon G. Sanders, Joshua Shorenstein, Hannes Holste, Pieter C. Dorrestein & Rob Knight
  2. Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
    Jose A. Navas-Molina, Hannes Holste & Rob Knight
  3. Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
    Austin D. Swafford, Stephanie B. Orchanian, Pieter C. Dorrestein & Rob Knight
  4. Department of Biology, University of California, San Diego, La Jolla, CA, USA
    Semar Petrus
  5. Department of Computer Science, University of Colorado, Boulder, Boulder, CO, USA
    Adam Robbins-Pianka
  6. Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
    Colin J. Brislawn
  7. Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
    Mingxun Wang & Pieter C. Dorrestein
  8. Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
    Jai Ram Rideout, Evan Bolyen, Matthew Dillon & J. Gregory Caporaso
  9. Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
    J. Gregory Caporaso

Authors

  1. Antonio Gonzalez
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  2. Jose A. Navas-Molina
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  3. Tomasz Kosciolek
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  4. Daniel McDonald
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  5. Yoshiki Vázquez-Baeza
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  6. Gail Ackermann
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  7. Jeff DeReus
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  8. Stefan Janssen
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  9. Austin D. Swafford
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  10. Stephanie B. Orchanian
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  11. Jon G. Sanders
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  12. Joshua Shorenstein
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  13. Hannes Holste
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  14. Semar Petrus
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  15. Adam Robbins-Pianka
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  16. Colin J. Brislawn
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  17. Mingxun Wang
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  18. Jai Ram Rideout
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  19. Evan Bolyen
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  20. Matthew Dillon
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  21. J. Gregory Caporaso
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  22. Pieter C. Dorrestein
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  23. Rob Knight
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Contributions

A.G., J.A.N.-M., T.K., D.M., Y.V.-B., G.A., J.D., S.J., A.D.S., S.B.O., J.G.S., J.S., H.H., S.P., A.R.-P., C.J.B., M.W., J.R.R., E.B., M.D., J.G.C., P.C.D., and R.K. implemented the Qiita main or the Qiita plugins code. A.G., J.A.N.-M., and Y.V.-B. conducted the example meta-analysis. All authors wrote the manuscript.

Corresponding author

Correspondence toRob Knight.

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The authors declare no competing interests.

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Gonzalez, A., Navas-Molina, J.A., Kosciolek, T. et al. Qiita: rapid, web-enabled microbiome meta-analysis.Nat Methods 15, 796–798 (2018). https://doi.org/10.1038/s41592-018-0141-9

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