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QIIME 2 user documentation

This site is the official user documentation for QIIME™ 2, including installation instructions, tutorials, and other important information. Visit for information on QIIME™ 1.


QIIME 2 is in its alpha release phase. Since it is alpha software, it is not necessarily stable or complete. Commands, functionality, interfaces, and documentation will change as the software reaches beta status. QIIME 1 is still the recommended platform for microbiome analyses as it is relatively stable, feature-complete, and supports high-performance computing environments. QIIME 1 will continue to be supported through the end of 2017 to allow QIIME 2 to stabilize and users to transition to using this new software. Please give QIIME 2 a try and let us know how it can be improved by getting in touch.

Getting started

Check out the getting started guide to begin using QIIME 2.