We are trying to determine good QIIME2 parameters for our kind of sequencing data and therefore testing different options.
So I was wondering the following:
Are you planning to integrate more parameters (like setDadaOpt parameters) from the DADA2 R package into QIIME2 soon?
If these parameters are not yet implemented in QIIME2, does this imply that they are not very important? Or that you should not play aroung (mess up) with them?
@Lou,
I am not a core developer on either of those packages, but am happy to speculate. Please take the following opinions with a hefty grain of salt. I suspect that the decision to provide a subset of DADA2 parameters in q2-dada2 was mostly about providing a simpler API for QIIME 2 users, while reducing the maintenance burden on the developers. So…
New parameters will probably be exposed in q2-dada2 on an as-needed basis. As you may have noticed, both of the topics you linked have been addressed and/or are planned for development. Both offered clear opportunities to improve user experience. If you have specific parameters you think would be beneficial to QIIME 2 users, feel free to start a discussion in a new “Ideas and Suggestions” topic here.
“Not frequently modified” and “not important” are very different things, and I’m going to bet that sensible defaults work for most DADA users, within and outside of QIIME 2. If those defaults don’t work for you, you should feel free to play around with them and see what you get. Exporting your data from QIIME 2 to experiment in the original DADA2 R package is likely the easiest way to do this. If you discover something important to analysis of your type of sequence data, please consider sharing what you’ve learned with the community.
Please take the following opinions with a hefty grain of salt. 
I suspect that the decision to provide a subset of DADA2 parameters in 