Hi all,
A few comments on various parts of this conversation:
We would like to, but on the QIIME 2 side we do rely on those QIIME-compatible Silva files that @William has typically been responsible for creating.
@William, I would be happy to try to help you and @SoilRotifer with this. It would be great if we could figure out how to automate this process, which would be easier if we had this functionality accessible in a QIIME 2 plugin.
As a side note, if your current processing workflow requires QIIME 1 for some steps, it's possible to install QIIME 1 and QIIME 2 side-by-side in different conda environments. If you already have QIIME 2 installed, you should be able to follow the QIIME 1 conda installation steps to get a working QIIME 1 base install. If the steps you need from QIIME 1 are focused on OTU clustering, QIIME 2 does now offer similar functionality (see here).
Please let me know what I can do to help in this process. It would be really great to get some trained classifiers for Silva 132 posted for use with QIIME 2.