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QIIME 2

microbiome multi-omics data science

QIIME 2™ (pronounced “chime two” 🔔) is a microbiome multi-omics bioinformatics and data science platform that is trusted, free, open source, extensible, and community developed and supported.

🙋 Get help, connect, and learn on the QIIME 2 Forum

The QIIME 2 Forum is your main resource for using QIIME 2. Running since 2016, with over 7000 registered users and over 500,000 page views per month, it’s the hub of the microbiome data science community. Find announcements of releases and workshops, discover or share microbiome-related jobs, and get technical support - all for free on the Forum. See the latest announcements below 👇.

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🧐 Learn to use QIIME 2

The QIIME 2 user documentation is where you can find tutorials and reference content. There is a lot of excellent content here, and it will soon be refactored in JupyterBook and with Diátaxis to improve the organization and update the content to highlight the newest functionality.

🎛️ QIIME 2 makes your data analysis as efficient and accessible as possible, for you

If you’re a data scientist or want to integrate QIIME 2 in your existing code, checkout the Python 3 or R API. If you prefer to work with command line tools, you can start with the command line interface. If you prefer a graphical interface, try using QIIME 2 through Galaxy (for example, at https://cancer.usegalaxy.org). You can access the same underlying analytic functionality regardless of which interface you choose, so you can pick the one that makes you most efficient.

📈 Interact with QIIME 2 results and explore how they were generated

The new QIIME 2 View is completed re-written, enabling us to bring new features to you quicker. For now, check out the new dynamic Visualization gallery and consider sharing some of your favorite QIIME 2 results with the community.

📓 Perform fully reproducible bioinformatics

Your analysis is complex - QIIME 2 records the steps you took to be sure that your work will be reproducible by you or others.

View the provenance of your (or anyone else’s) QIIME 2 result using QIIME 2 View or Provenance Replay by running:

$ qiime tools replay-provenance \
    --in-fp l6-ancom-subject.qzv \
    --out-fp my-datas-provenance.bash

🔌 Build, support, and publish your own QIIME 2 plugins

Developing with QIIME 2 is your main resource for learning QIIME 2 plugin development, starting with a 7 lesson tutorial where you’ll build your first QIIME 2 plugin from scratch. New content is added regularly.

📚 Discover tools built by others!

Coming soon: We are currently refactoring the QIIME 2 Library to make it more useful for developers and users. More on this throughout 2024!

🙏 Funding

QIIME 2 is funded in part by NIH National Cancer Institute Informatics Technology for Cancer Research grant 1U24CA248454-01, and by grant DAF2019-207342 from the Chan Zuckerberg Initiative (CZI) DAF, an advised fund of Silicon Valley Community Foundation (CZI grant DOI: 10.37921/862772dbrrej; funder DOI 10.13039/100014989).

This website was built with MyST Markdown, which is supported in part with funding from the Alfred P. Sloan Foundation.

Initial support for the development of QIIME 2 was provided through a grant from the National Science Foundation.

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