QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.

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Automatically track your analyses with decentralized data provenance — no more guesswork on what commands were run!

Interactively explore your data with beautiful visualizations that provide new perspectives.

Easily share results with your team, even those members without QIIME 2 installed.

Plugin-based system — your favorite microbiome methods all in one place.


Choose the interface that fits your needs

q2cli the command line interface

Artifact API the data scientist's interface

q2studio the graphical user interface (PROTOTYPE)

q2studio is a functional prototype of a graphical user interface for QIIME 2, and is not necessarily feature-complete with respect to q2cli and the Artifact API.

Citing QIIME 2

If you use QIIME 2 for any published research, please include the following citation:

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet C, 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 E, Da Silva R, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley G, Janssen S, Jarmusch AK, Jiang L, Kaehler B, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MG, Lee J, Ley R, Liu Y, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton J, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson, II 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 JJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CH, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. 2018. QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science. PeerJ Preprints 6:e27295v2 https://doi.org/10.7287/peerj.preprints.27295v2

QIIME 2 plugins frequently utilize other software packages that must be cited in addition to QIIME 2 itself. Run qiime tools citations on an Artifact or Visualization to discover all of the citations relevant to the creation of that result. Lists of citations are provided by https://view.qiime2.org as well. To generate the list of citations for a QIIME 2 Artifact or Visualization, navigate to the "Provenance" page, and then to the "Citations" tab.