Installing QIIME 2 using WSL¶
Warning
This site has been replaced by the new QIIME 2 “amplicon distribution” documentation, as of the 2025.4 release of QIIME 2. You can still access the content from the “old docs” here for the QIIME 2 2024.10 and earlier releases, but we recommend that you transition to the new documentation at https://amplicon-docs.qiime2.org. Content on this site is no longer updated and may be out of date.
Are you looking for:
the QIIME 2 homepage? That’s https://qiime2.org.
learning resources for microbiome marker gene (i.e., amplicon) analysis? See the QIIME 2 amplicon distribution documentation.
learning resources for microbiome metagenome analysis? See the MOSHPIT documentation.
installation instructions, plugins, books, videos, workshops, or resources? See the QIIME 2 Library.
general help? See the QIIME 2 Forum.
Old content beyond this point… 👴👵
Please see the official Microsoft guide to install and set up the WSL. Once you have installed and set up the WSL, install a Linux distribution (step 6 of the WSL guide). We suggest the latest stable version of Ubuntu.
Once you have set up the WSL, you can follow the native conda installation guide, choosing the Windows (via WSL) instructions to finish setting up QIIME 2.
Please check out the QIIME 2 Forum for Community Contributions related to setting up and using the WSL.