# qiime2 (the QIIME 2 framework)

![](https://github.com/qiime2/qiime2/workflows/ci-dev/badge.svg)

Source code repository for the QIIME 2 framework.

QIIME 2™ is a powerful, extensible, and decentralized microbiome bioinformatics
platform that is free, open source, and community developed. With a focus on
data and analysis transparency, QIIME 2 enables researchers to start an
analysis with raw DNA sequence data and finish with publication-quality figures
and statistical results.

Visit [https://qiime2.org](https://qiime2.org) to learn more about the QIIME 2
project.

## Installation

Detailed instructions are available in the
[documentation](https://docs.qiime2.org/).

## Users

Head to the [user docs](https://docs.qiime2.org/) for help getting started,
core concepts, tutorials, and other resources.

Just have a question? Please ask it in our
[forum](https://forum.qiime2.org/c/user-support).

## Developers

Please visit the [contributing page](https://dev.qiime2.org) for more
information on contributions, documentation links, and more.

## 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 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, and Caporaso JG. 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology 37:852–857. https://doi.org/10.1038/s41587-019-0209-9
