Users frequently ask about the current status of QIIME 2, and whether it should be used for their data analyses. As of the 2017.8 release, QIIME 2 is no longer in alpha release status. Users can confidently use QIIME 2 and the plugins in the core distribution. These methods are tested, and should work as well, and in most cases better than, their QIIME 1 equivalents.
QIIME 2 will succeed QIIME 1 on January 1, 2018. QIIME 1 will no longer be supported at that time, as development and support effort for QIIME will be focused entirely on QIIME 2. We recommend that existing QIIME users begin transitioning from QIIME 1 to QIIME 2 now.
As a QIIME 2 user, there are a few things to be aware of:
At this time, there is some QIIME 1 functionality that is not yet implemented in QIIME 2. We plan to achieve useful feature parity with QIIME 1 by the end of 2017. We maintain a list of the functionality that we plan to port from QIIME 1. If you have questions, comments, or suggestions about this, please post them to the QIIME 2 Forum.
Some interfaces may change over the next few releases. We’re still making changes to how QIIME 2 works, and as a result there may be changes to how commands are run, the names of actions or parameters, and default value settings. We attempt to document all of these changes in our release notes – please be sure to review the release notes so that you’re aware of these changes.
As always, thanks for supporting the QIIME 2 project!