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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This site has been replaced by the new QIIME 2 “amplicon distribution” documentation, as of the 2025.4 release of QIIME 2.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 Content on this site is no longer updated and may be out of date.

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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.