Welcome! 👋 This is the primary documentation introducing the use of QIIME 2 for marker gene (i.e., amplicon) based microbiome analysis.
Based on our website analytics, these are the questions that most frequently drive readers to our documentation:
I’m completely new to QIIME 2. Where should I start?
We recommend that all newcomers read Getting started with QIIME 2 for a high-level discussion about what QIIME 2 is, an introduction to concepts that will help you understand QIIME 2 quickly, and references to resources you can use for learning.
How can I analyze my data with QIIME 2?
Historically, the Moving Pictures tutorial 🎥 is the resource that most users have started with to learn how to use QIIME 2. More recently, we’ve developed the Gut-to-soil axis tutorial 💩🌱. Both are written for readers who are also new to microbiome analysis. If you’re already familiar with microbiome analysis but new to QIIME 2, we recommend also looking at QIIME 2 for experienced microbiome researchers and Conceptual overview of marker gene (i.e., amplicon) data analysis.
How do I install QIIME 2?
To install the amplicon distribution of QIIME 2, refer to the instructions on the QIIME 2 Library.
Where can I find reference materials or other resources?
If you’re looking for reference material on the plugins and actions installed in the QIIME 2 amplicon distribution, see Available plugins. If you’re looking for data resources, such as pre-trained taxonomic classifiers, see Data Resources on the QIIME 2 Library website. If you’re looking for other tools available for the QIIME 2 Framework (Q2F), see Plugins on the QIIME 2 Library.
How should I prepare my metadata?
See our documentation of the Metadata file format.
Where can I find help?
Head over to the QIIME 2 Forum, where you can browse nearly 10 years of discussion, questions, and answers related to microbiome data science with QIIME 2. You can ask your own questions if you don’t find existing answers, and give back by answering someone else’s questions when you’re ready.
Where can I find announcements and other news?
Important announcements (e.g., new releases, bug reports, upcoming changes) are shared through the Announcements feed on the QIIME 2 Forum. If you register for a (free) account, you can get those announcements by email. Alternatively, you can subscribe by RSS.
For other topics, read on...
Navigating this documentation¶
This documentation is organized under the Diátaxis framework for technical documentation, which categorizes content into sections containing Tutorials, How-To-Guides, Explanations, and References. Each serves a different goal for the reader:
| Chapter | Purpose |
|---|---|
| Tutorials | Provide a guided exploration of a topic for learning. |
| How To Guides | Provide step-by-step instructions on how to accomplish specific goals. |
| Explanations | Provide a discussion intended to aid in understanding a specific topic. |
| References | Provide specific information (e.g., the list of available plugins). |
Contributors¶
This documentation is the result of past, present, and future (🤞) collaborative efforts.
The authors would like to thank those who have contributed to the writing of the original QIIME 2 User Documentation, as well as those who have contributed to this documentation. Some of the content in this documentation is sourced directly from the older material.
The QIIME 2 Forum moderators and community members have also been instrumental to the development of ideas and content presented here.
Funding 🙏¶
This work was funded in part by NIH National Cancer Institute Informatics Technology for Cancer Research grant 1U24CA248454-01.
This documentation is built with MyST Markdown and Jupyter Book, which are 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.
Citing QIIME 2¶
If you use QIIME 2 in your work, please cite Bolyen, Rideout, Dillon, Bokulich, et al (2019), as well as the underlying tools that are used by QIIME 2.
To get a list of citations that are specifically relevant to a QIIME 2 Result you created (i.e., a .qza or .qzv), load that Result with QIIME 2 View and navigate to the Citations tab.
License¶
Microbiome Marker Gene Analysis with QIIME 2 (©2025) and the project’s predecessors have many Contributors. Content development and maintenance is led by the Caporaso Lab at Northern Arizona University. This content is licensed under CC BY-NC-ND 4.0
- 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. 10.1038/s41587-019-0209-9