q2-dada2 and NextSeq amplicon data

[Nicholas_Bokulich]

Hi @ctekellogg ,
Just to add to @buzic 's advice: it should be fine to use q2-dada2 for denoising Nextseq data, but carefully check outputs as always. See here (the answer from the dada2 developer in the topic that @buzic shared):

NovaSeq and Dada2 incompatibility.

i wanted to add to this thread my perspective as developer/maintainer of the DADA2 software package. We think DADA2 works fine with binned-quality-score data such as NovaSeq, at least in the vast majority of cases. While there are some oddities when inspecting the error model that DADA2 learns from binned quality scores, there don't seem to be oddities when evaluating the results of denoising on NovaSeq (with the caveat that this is based on a relatively limited number of test samples). Further…