QIIME 2 is an AI-ready microbiome multi-omics data science platform
Trusted, free, open source, extensible, and community developed and supported bioinformatics.
Features
Our users love these features
The QIIME 2 Framework (Q2F) empowers researchers to conduct reproducible biological data science through a variety of interfaces and using diverse methods.
Latest Methods
QIIME 2 integrates dozens of plugins and hundreds of bioinformatics methods, allowing users to perform cutting-edge microbiome analysis with interactive visualizations and robust statistical tools.
Automated Provenance Recording
All commands, parameters, and computational environments used during analysis are automatically recorded with decentralized data provenance. This ensures full transparency and reproducibility. With data provenance embedded as metadata in your data and visualizations, your data won’t become disconnected from the details of how it was created.
Multiple Interfaces
All analytic functionality is available through multiple interfaces: Python 3 and R APIs for programmatic access; a command line interface (CLI) for efficient scripting, and a graphical interface (GUI) via Galaxy for an intuitive, visual experience. Regardless of your computational background, QIIME 2 has an interface that will enable you to work efficiently!
Extensible
Q2F is plugin-based, making it straight-forward to extend and customize the platform. Developers can integrate their bioinformatics methods, leveraging an extensive library of existing functionality and leaving the interfaces and provenance recording to the framework.
Accessible
QIIME 2 is designed to be accessible to all users, from students to seasoned researchers. It provides simplified workflows, comprehensive tutorials, and clear documentation to streamline microbiome analysis. Visit the QIIME 2 Library for guides, tutorials, and reference materials.
Open Source Community
QIIME 2 thrives because of its community, which drives the direction of the project. The QIIME 2 Forum is the hub of the community, and serves as a free resource for discussions, troubleshooting, and collaboration. Users are encouraged to engage and share their insights. You can learn about our expectations of community members in the code of conduct.
Distributions
Multi-Omics
The QIIME 2 Framework supports expanding -omics data types through specialized distributions.
Amplicon
A suite of plugins that provide broad analytic functionality to support microbiome marker gene analysis from raw sequencing data through publication quality visualizations and statistics.
MOSHPIT
MOSHPIT (MOdular SHotgun metagenome Pipelines with Integrated provenance Tracking) is a toolkit of plugins for whole metagenome assembly, annotation, and analysis.
Pathogenome
A suite of plugins to detect viral genomes and protein sequences from MAGs and contigs for antimicrobial-resistance.
Tiny
A minimal installation of the QIIME 2 Framework for developers that is intended to be extended with custom functionality and plugins.
FAQs
Frequently Asked Questions
How do I pronounce QIIME 2?
QIIME 2 is pronounced “chime two”. It is an AI-ready microbiome multi-omics data science platform that is free, open source, extensible, and community-developed. QIIME 2 enables researchers to conduct reproducible microbiome analysis using a variety of interfaces and tools.
Is QIIME 2 free to use?
Yes! QIIME 2 is completely free and open source, meaning anyone can use, modify, and contribute to its development under our BSD 3-Clause License. That includes commercial use.
Is it difficult to install and use QIIME 2?
Not at all!
- If you have QIIME 2 results and want to interact with them without installing QIIME 2, use QIIME 2 View.
- If you want to install and use QIIME 2 on your own system, follow the installation guide.
To learn marker gene (i.e., amplicon) analysis with QIIME 2, see the amplicon docs. To learn metagenome (i.e., shotgun) analysis with QIIME 2, see the MOSHPIT docs. To learn advanced techniques for working with the QIIME 2 Framework, see Using QIIME 2. To build and distribute your own plugins, see Developing with QIIME 2. As of March 2025, we’re doing an extensive re-write of our documentation using JupyterBook and Diátaxis to modernize it and to improve organization and accessibility.
Will my data survive the test of time?
Yes! All data generated by QIIME 2 is stored in .zip files. The file extensions .qza and .qzv stand for QIIME Zipped Artifact and QIIME Zipped Visualization. You can open them with any unzip utility, such as unzip.
We call these “archives”, and they contain your data in the normal formats (.fastq.gz, .fasta, .biom, …). Additionally, these archives have embedded provenance which means that even without QIIME 2 you will still have precise details on how the data was generated. There is no need to keep a centralized database (or distributed blockchain) online for 20 years: the provenance always lives with your data inside the zip file. You can learn about the archive format here.
What makes QIIME 2 extensible? Can I customize it to fit my work?
The professionally engineered architecture of QIIME 2 makes it an extremely modular and customizable tool.
The QIIME 2 Framework (Q2F) provides the general purpose data science functionality, like data provenance tracking, and serves as the glue between plugins and the many interfaces. The plugins provide all analytic functionality, and you can have as many of these as you need. Groups of plugins that are intended to be used together are shared as distributions, which makes it easy to get started right away with the most common workflows.
How can I get help or become involved with the QIIME 2 community?
The QIIME 2 Forum is the primary resource for support and community interaction. There you can find announcements, job postings, and technical assistance from a vibrant and active microbiome data science community.
If you’re not a software developer and want to get involved in the project, see How to Get Involved in the QIIME 2 Community. If you are a developer and want to get involved in the project, see our Contributing Guide.
What do you mean by "AI-Ready"?
We mean that you’ll always know how the QIIME 2 Artifacts that you’re working with were generated (because of Q2F’s data provenance recording), and that the steps performed to create them made logical sense (because of Q2F’s Artifact Class system). We are now working on functionality that allows users to sign and add a license to their data, so you’ll always know if or how it can be used.
Garbage In, Garbage Out. Artifacts In, Actual Intelligence Out.
Where can I find more QIIME 2 plugins?
The QIIME 2 Library hosts a variety of plugins and tools developed by the community, expanding QIIME 2’s capabilities beyond its base distributions. You can also refer to Community Contributions on the QIIME 2 Forum.
funding
Support from federal and foundation grants
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).
QIIME 2’s documentation is (mostly) 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.