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., ... Caporaso, J. G. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37(8), 852-857. https://doi.org/10.1038/s41587-019-0209-9
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, 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, CHD, Willis, AD, Xu, ZZ, Zaneveld, JR, Zhang, Y, Zhu, Q, Knight, R & Caporaso, JG 2019, 'Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2', Nature Biotechnology, vol. 37, no. 8, pp. 852-857. https://doi.org/10.1038/s41587-019-0209-9
@article{82a0c8be45a0445da7128cd28cbaa539,
title = "Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2",
author = "Evan Bolyen and Rideout, {Jai Ram} and Dillon, {Matthew R.} and Bokulich, {Nicholas A.} and Abnet, {Christian C.} and Al-Ghalith, {Gabriel A.} and Harriet Alexander and Alm, {Eric J.} and Manimozhiyan Arumugam and Francesco Asnicar and Yang Bai and Bisanz, {Jordan E.} and Kyle Bittinger and Asker Brejnrod and Brislawn, {Colin J.} and Brown, {C. Titus} and Callahan, {Benjamin J.} and Caraballo-Rodr{\'i}guez, {Andr{\'e}s Mauricio} and John Chase and Cope, {Emily K.} and {Da Silva}, Ricardo and Christian Diener and Dorrestein, {Pieter C.} and Douglas, {Gavin M.} and Durall, {Daniel M.} and Claire Duvallet and Edwardson, {Christian F.} and Madeleine Ernst and Mehrbod Estaki and Jennifer Fouquier and Gauglitz, {Julia M.} and Gibbons, {Sean M.} and Gibson, {Deanna L.} and Antonio Gonzalez and Kestrel Gorlick and Jiarong Guo and Benjamin Hillmann and Susan Holmes and Hannes Holste and Curtis Huttenhower and Huttley, {Gavin A.} and Stefan Janssen and Jarmusch, {Alan K.} and Lingjing Jiang and Kaehler, {Benjamin D.} and Kang, {Kyo Bin} and Keefe, {Christopher R.} and Paul Keim and Kelley, {Scott T.} and Dan Knights and Irina Koester and Tomasz Kosciolek and Jorden Kreps and Langille, {Morgan G.I.} and Joslynn Lee and Ruth Ley and Liu, {Yong Xin} and Erikka Loftfield and Catherine Lozupone and Massoud Maher and Clarisse Marotz and Martin, {Bryan D.} and Daniel McDonald and McIver, {Lauren J.} and Melnik, {Alexey V.} and Metcalf, {Jessica L.} and Morgan, {Sydney C.} and Morton, {Jamie T.} and Naimey, {Ahmad Turan} and Navas-Molina, {Jose A.} and Nothias, {Louis Felix} and Orchanian, {Stephanie B.} and Talima Pearson and Peoples, {Samuel L.} and Daniel Petras and Preuss, {Mary Lai} and Elmar Pruesse and Rasmussen, {Lasse Buur} and Adam Rivers and Robeson, {Michael S.} and Patrick Rosenthal and Nicola Segata and Michael Shaffer and Arron Shiffer and Rashmi Sinha and Song, {Se Jin} and Spear, {John R.} and Swafford, {Austin D.} and Thompson, {Luke R.} and Torres, {Pedro J.} and Pauline Trinh and Anupriya Tripathi and Turnbaugh, {Peter J.} and Sabah Ul-Hasan and {van der Hooft}, {Justin J.J.} and Fernando Vargas and Yoshiki V{\'a}zquez-Baeza and Emily Vogtmann and {von Hippel}, Max and William Walters and Yunhu Wan and Mingxun Wang and Jonathan Warren and Weber, {Kyle C.} and Williamson, {Charles H.D.} and Willis, {Amy D.} and Xu, {Zhenjiang Zech} and Zaneveld, {Jesse R.} and Yilong Zhang and Qiyun Zhu and Rob Knight and Caporaso, {J. Gregory}",
note = "Funding Information: 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. Thanks to the Yellowstone Center for Resources for research permit no. 5664 to J.R.S. for Yellowstone access and sample collection. We thank P. J. McMurdie for helpful discussion on the relationships between QIIME 2 and phyloseq. We would like to thank the users of QIIME 1 and 2, whose invaluable feedback has shaped QIIME 2. In particular, we would like to thank A. Abdelfattah (Stockholm University, Sweden), R. C. T. Boutin (University of British Columbia, Canada), D. J. Bradshaw II (Florida Atlantic University Harbor Branch Oceanographic Institute, USA), L. Bullington (MPG Ranch, USA), J. W. Debelius (Karolinska Institutet, Sweden), C. Duvallet (Massachusetts Institute of Technology, USA), E. Korzune Ganda (Cornell University, USA), A. Mahnert (Medical University of Graz, Austria), M. C. Melendrez (St. Cloud State University, USA), D. O{\textquoteright}Rourke (University of New Hampshire, USA), A. R. Rivers (USDA ARS, USA), B. Sen (Tianjin University, China), S. Tangedal (Haukeland University Hospital and University of Bergen, Norway), P. J. Torres (San Diego State University, USA) and J. Warren (National Laboratory Service, UK) for writing end-user reviews included in the Supplementary Methods.",
year = "2019",
month = aug,
day = "1",
doi = "10.1038/s41587-019-0209-9",
language = "English",
volume = "37",
pages = "852--857",
journal = "Nature Biotechnology",
issn = "1087-0156",
publisher = "Nature Publishing Group",
number = "8",
}
TY - JOUR
T1 - Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
AU - Bolyen, Evan
AU - Rideout, Jai Ram
AU - Dillon, Matthew R.
AU - Bokulich, Nicholas A.
AU - Abnet, Christian C.
AU - Al-Ghalith, Gabriel A.
AU - Alexander, Harriet
AU - Alm, Eric J.
AU - Arumugam, Manimozhiyan
AU - Asnicar, Francesco
AU - Bai, Yang
AU - Bisanz, Jordan E.
AU - Bittinger, Kyle
AU - Brejnrod, Asker
AU - Brislawn, Colin J.
AU - Brown, C. Titus
AU - Callahan, Benjamin J.
AU - Caraballo-Rodríguez, Andrés Mauricio
AU - Chase, John
AU - Cope, Emily K.
AU - Da Silva, Ricardo
AU - Diener, Christian
AU - Dorrestein, Pieter C.
AU - Douglas, Gavin M.
AU - Durall, Daniel M.
AU - Duvallet, Claire
AU - Edwardson, Christian F.
AU - Ernst, Madeleine
AU - Estaki, Mehrbod
AU - Fouquier, Jennifer
AU - Gauglitz, Julia M.
AU - Gibbons, Sean M.
AU - Gibson, Deanna L.
AU - Gonzalez, Antonio
AU - Gorlick, Kestrel
AU - Guo, Jiarong
AU - Hillmann, Benjamin
AU - Holmes, Susan
AU - Holste, Hannes
AU - Huttenhower, Curtis
AU - Huttley, Gavin A.
AU - Janssen, Stefan
AU - Jarmusch, Alan K.
AU - Jiang, Lingjing
AU - Kaehler, Benjamin D.
AU - Kang, Kyo Bin
AU - Keefe, Christopher R.
AU - Keim, Paul
AU - Kelley, Scott T.
AU - Knights, Dan
AU - Koester, Irina
AU - Kosciolek, Tomasz
AU - Kreps, Jorden
AU - Langille, Morgan G.I.
AU - Lee, Joslynn
AU - Ley, Ruth
AU - Liu, Yong Xin
AU - Loftfield, Erikka
AU - Lozupone, Catherine
AU - Maher, Massoud
AU - Marotz, Clarisse
AU - Martin, Bryan D.
AU - McDonald, Daniel
AU - McIver, Lauren J.
AU - Melnik, Alexey V.
AU - Metcalf, Jessica L.
AU - Morgan, Sydney C.
AU - Morton, Jamie T.
AU - Naimey, Ahmad Turan
AU - Navas-Molina, Jose A.
AU - Nothias, Louis Felix
AU - Orchanian, Stephanie B.
AU - Pearson, Talima
AU - Peoples, Samuel L.
AU - Petras, Daniel
AU - Preuss, Mary Lai
AU - Pruesse, Elmar
AU - Rasmussen, Lasse Buur
AU - Rivers, Adam
AU - Robeson, Michael S.
AU - Rosenthal, Patrick
AU - Segata, Nicola
AU - Shaffer, Michael
AU - Shiffer, Arron
AU - Sinha, Rashmi
AU - Song, Se Jin
AU - Spear, John R.
AU - Swafford, Austin D.
AU - Thompson, Luke R.
AU - Torres, Pedro J.
AU - Trinh, Pauline
AU - Tripathi, Anupriya
AU - Turnbaugh, Peter J.
AU - Ul-Hasan, Sabah
AU - van der Hooft, Justin J.J.
AU - Vargas, Fernando
AU - Vázquez-Baeza, Yoshiki
AU - Vogtmann, Emily
AU - von Hippel, Max
AU - Walters, William
AU - Wan, Yunhu
AU - Wang, Mingxun
AU - Warren, Jonathan
AU - Weber, Kyle C.
AU - Williamson, Charles H.D.
AU - Willis, Amy D.
AU - Xu, Zhenjiang Zech
AU - Zaneveld, Jesse R.
AU - Zhang, Yilong
AU - Zhu, Qiyun
AU - Knight, Rob
AU - Caporaso, J. Gregory
N1 - Funding Information:
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. Thanks to the Yellowstone Center for Resources for research permit no. 5664 to J.R.S. for Yellowstone access and sample collection. We thank P. J. McMurdie for helpful discussion on the relationships between QIIME 2 and phyloseq. We would like to thank the users of QIIME 1 and 2, whose invaluable feedback has shaped QIIME 2. In particular, we would like to thank A. Abdelfattah (Stockholm University, Sweden), R. C. T. Boutin (University of British Columbia, Canada), D. J. Bradshaw II (Florida Atlantic University Harbor Branch Oceanographic Institute, USA), L. Bullington (MPG Ranch, USA), J. W. Debelius (Karolinska Institutet, Sweden), C. Duvallet (Massachusetts Institute of Technology, USA), E. Korzune Ganda (Cornell University, USA), A. Mahnert (Medical University of Graz, Austria), M. C. Melendrez (St. Cloud State University, USA), D. O’Rourke (University of New Hampshire, USA), A. R. Rivers (USDA ARS, USA), B. Sen (Tianjin University, China), S. Tangedal (Haukeland University Hospital and University of Bergen, Norway), P. J. Torres (San Diego State University, USA) and J. Warren (National Laboratory Service, UK) for writing end-user reviews included in the Supplementary Methods.
PY - 2019/8/1
Y1 - 2019/8/1
UR - http://www.scopus.com/inward/record.url?scp=85069676260&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85069676260&partnerID=8YFLogxK
U2 - 10.1038/s41587-019-0209-9
DO - 10.1038/s41587-019-0209-9
M3 - Letter
C2 - 31341288
AN - SCOPUS:85069676260
SN - 1087-0156
VL - 37
SP - 852
EP - 857
JO - Nature Biotechnology
JF - Nature Biotechnology
IS - 8
ER -