Hello
Is there any options for OTU picking in Qiime2? Or, in other words, what functions from Qiime1 have carried over and what are they called now? I am very stuck.
Thanks
Laura
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!
One follow-up on @thermokarst’s reply. This paper has a good discussion of sequence variants versus OTU clusters for microbiome analysis if you’d like some more background on the difference. We will however be adding options for OTU picking in the near future - these should be available in the 2017.8 release (due out later this month), or in the worst case in the 2017.9 release (in September).
Sorry to hear that you’re having trouble with the transition. As @thermokarst mentioned, be sure to spend some time in the documentation (here’s the Getting Started Guide).
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vsearch-based OTU picking is now available in the 2017.9 release! 
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