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PreprintCited by 838

The DOI matches its Crossref record.

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

Open access
Bolyen, Evan, Rideout, Jai Ram, Dillon, Matthew R, Bokulich, Nicholas A, Abnet, Christian, 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, Chase, John, Cope, Emily, Da Silva, Ricardo, Dorrestein, Pieter C, Douglas, Gavin M, Durall, Daniel M, Duvallet, Claire, Edwardson, Christian F, Ernst, Madeleine, Estaki, Mehrbod, Fouquier, Jennifer, Gauglitz, Julia M, Gibson, Deanna L, Gonzalez, Antonio, Gorlick, Kestrel, Guo, Jiarong, Hillmann, Benjamin, Holmes, Susan, Holste, Hannes, Huttenhower, Curtis, Huttley, Gavin, Janssen, Stefan, Jarmusch, Alan K, Jiang, Lingjing, Kaehler, Benjamin, Kang, Kyo Bin, Keefe, Christopher R, Keim, Paul, Kelley, Scott T, Knights, Dan, Koester, Irina, Kosciolek, Tomasz, Kreps, Jorden, Langille, Morgan GI, Lee, Joslynn, Ley, Ruth, Liu, Yong-Xin, Loftfield, Erikka, Lozupone, Catherine, Maher, Massoud, Marotz, Clarisse, Martin, Bryan D, McDonald, Daniel, McIver, Lauren J, Melnik, Alexey V, Metcalf, Jessica L, Morgan, Sydney C, Morton, Jamie, Naimey, Ahmad Turan, Navas-Molina, Jose A, Nothias, Louis Felix, Orchanian, Stephanie B, Pearson, Talima, Peoples, Samuel L, Petras, Daniel, Preuss, Mary Lai, Pruesse, Elmar, Rasmussen, Lasse Buur, Rivers, Adam, Robeson, II, Michael S, Rosenthal, Patrick, Segata, Nicola, Shaffer, Michael, Shiffer, Arron, Sinha, Rashmi, Song, Se Jin, Spear, John R, Swafford, Austin D, Thompson, Luke R, Torres, Pedro J, Trinh, Pauline, Tripathi, Anupriya, Turnbaugh, Peter J, Ul-Hasan, Sabah, van der Hooft, Justin JJ, Vargas, Fernando, Vázquez-Baeza, Yoshiki, Vogtmann, Emily, von Hippel, Max, Walters, William, Wan, Yunhu, Wang, Mingxun, Warren, Jonathan, Weber, Kyle C, Williamson, Chase HD, Willis, Amy D, Xu, Zhenjiang Zech, Zaneveld, Jesse R, Zhang, Yilong, Knight, Rob, Caporaso, J Gregory·2018
DOI 10.7287/peerj.preprints.27295v1
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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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Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, 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., Da Silva, R., Dorrestein, P. C., Douglas, G. M., Durall, D. M., Duvallet, C., Edwardson, C. F., Ernst, M., Estaki, M., Fouquier, J., Gauglitz, J. M., Gibson, D. L., Gonzalez, A., Gorlick, K., Guo, J., Hillmann, B., Holmes, S., Holste, H., Huttenhower, C., Huttley, G., Janssen, S., Jarmusch, A. K., Jiang, L., Kaehler, B., Kang, K. B., Keefe, C. R., Keim, P., Kelley, S. T., Knights, D., Koester, I., Kosciolek, T., Kreps, J., Langille, M. G., 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., 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, II, 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., Vargas, F., Vázquez-Baeza, Y., Vogtmann, E., von Hippel, M., Walters, W., Wan, Y., Wang, M., Warren, J., Weber, K. C., Williamson, C. H., Willis, A. D., Xu, Z. Z., Zaneveld, J. R., Zhang, Y., Knight, R., & Caporaso, J. G.
Publisher
PeerJ
Published
2018-10-24
DOI
10.7287/peerj.preprints.27295v1
OpenAlex
W2897204056
Cited by
838
References
0
Type
posted content
Language
en
Open access
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CoChat. (2026). Citation check: QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science. https://app.cochat.ai/papers/10.7287/peerj.preprints.27295v1
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Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, 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., . . . Caporaso, J. G. (2018). QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science. https://doi.org/10.7287/peerj.preprints.27295v1

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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

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