Does Qiime2 still offer Qiime1-like pipelines?

Hi @LauraMason, thanks for reaching out!

Currently we're not doing any OTU picking in QIIME 2, but instead we are working with "sequence variants" (i.e. 100% OTUs). Generally speaking we treat the downstream analyses mostly the same as OTUs when using sequence variants.

QIIME 2 is a complete rewrite of QIIME, so a lot of the new functionality isn't just a rename from a QIIME 1 script. You can view a list of available plugins, and the methods and visualizations that they provide on the docs! As well, we have a working document that we are using to track future plugin development. Also, @gregcaporaso has a great post here that discusses the current status of QIIME 2.

I am really sorry to hear that! I hope this reply helps clarify things a little bit. If you are still stuck, or need help with anything else, please reach out to us here on the forum! Also, if you haven't already worked through the "Moving Pictures" tutorial, I would recommend starting there --- we have a lot of info in that document describing a typical QIIME 2 analysis. From there, we have a few other tutorials!