q2-dada2 and NextSeq amplicon data

[ctekellogg (Colleen Kellogg)]

Hi!
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!
Colleen

[buzic (Victoria)]

HI @ctekellogg

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.

Best,

Vic

[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…

[ctekellogg (Colleen Kellogg)]

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

Colleen