q2-dada2 and NextSeq amplicon data

I've typically used a MiSeq for our amplicon sequencing runs but we are currently trialling using a NextSeq as well. Now, I am processing my first NextSeq run of 16S-V4V5 amplicon data from the NextSeq and came across this forum post:

Strange Interactive Quality Plot after Importing the data - #9 by Mehrbod_Estaki?

Is it still recommended to use the R implementation of dada2 for NextSeq Runs or has the dada2 plugin for QIIME2 ben updated to make denoising (using dada2) NextSeq amplicon data ok?

Thank you!

HI @ctekellogg :wave:

I think the NextSeq and the NovaSeq have the same quality binning and 2 colour chemisty. So what applies to one would apply to the other regarding denoising. There is a really good breakdown of NovaSeq processing issues here. I hope thats helpful.

Basically, I don't think you can't use dada2 - but you are correct in that it has some issues associated with it. I am unsure if the development team of Qiime2 have implimented anything along these lines.


Vic :smiley:

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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):


Awesome. Thank you both! I appreciate your quick responses and resources provided.