Using QIIME 2

Your guide to becoming a QIIME 2 Framework power user.

Start reading here 👋¶

We know that you’re interested in QIIME 2 primarily for the latter - to achieve specific analysis goals related to microbiome data science - so we’ll start by providing references to where you can find that information. Generally, the QIIME 2 Library Stacks are the place to go to find links to all of the documentation sources.

Distribution documentation¶

If you’re looking for documentation on how to analyze microbiome marker gene (i.e., amplicon) data, you should refer to the QIIME 2 amplicon distribution documentation. That documentation is in transition and can now be found at https://amplicon-docs.qiime2.org.

If you want to analyze microbiome metagenomic data, refer to the MOSHPIT documentation at https://moshpit.qiime2.org. (MOSHPIT was referred to as the QIIME 2 metagenome distribution during its early development.)

If you’re looking for documentation on the tiny distribution, you’re most likely interested in plugin development. Welcome! Your best reference will be Developing with QIIME 2, our free, online Research Software Engineering text.

Plugin documentation¶

Stand-alone plugins are those that are not included in existing distributions, and these will generally provide their own documentation linked from the QIIME 2 Library. The list of these is growing, but some current (as of 28 February 2025) examples include:

• q2-micom
• genome-sampler
• q2-metnet
• q2-boots
• q2-amrfinderplus
• q2-fmt

Dataset-specific documentation¶

We expect to increasingly have documentation that is focused on analysis of specific interesting data sets. Good examples are the new gut-to-soil tutorial and the classic Moving Pictures tutorial. These will sometimes cross distributions and stand-alone plugins, for example integrating tools from MOSHPIT, q2-boots, and perhaps even metabolomics plugins, to illustrate microbiome multi-omics analysis workflows.

QIIME 2 Framework (Q2F) documentation 💃🏻¶

So what is Using QIIME 2?

Using QIIME 2 serves as a source for you to refer to when you need to accomplish specific tasks that are general to using the QIIME 2 Framework (Q2F). The distributions and plugins described above are all built on Q2F, so Using QIIME 2 presents information that is general to all of them. That includes things like using Artifacts as metadata, replaying provenance, creating and using an artifact cache, configuring and using our Parsl-based parallel computing framework, and more.

Using QIIME 2 will also include chapters that can help you understand the system when you want to go deeper, including things like what QIIME 2 Artifacts (e.g., .qza files) and Visualizations (e.g., .qzv files) are, and why you need to import your data before using QIIME 2. Understanding these topics will help you carry out advanced biological data science workflows and manage the corresponding data, but they aren’t strictly necessary for performing data with tools that build on QIIME 2.

If you’re ready to become a QIIME 2 Framework power user, read on...

Organization of Using QIIME 2¶

Using QIIME 2 is organized under the Diátaxis framework, which categorizes content into sections containing Tutorials, How-To-Guides, Explanations, and References. Each serves a different goal for the reader:

You can navigate these sections on the left sidebar.

Getting Help¶

For the most up-to-date information on how to get help with QIIME 2, as a user or developer, see here.

Funding 🙏¶

This work was funded in part by NIH National Cancer Institute Informatics Technology for Cancer Research grant 1U24CA248454-01.

This book 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.

License¶

Using QIIME 2 led by Greg Caporaso is licensed under CC BY-NC-ND 4.0.