Dear All,
I have been analysing NovaSeq 6000 16s rRNA V4-V5 data for the past few months. This is my first experience with NGS data analysis. As a novice, I was sideswiped by the fact that NovaSeq results were very different due to their binned quality scores. From multiple posts, the consensus is that Dada2 is not appropriate for NovaSeq sequences unless you can enforce monotonicity.
This leads me to the question, has Qiime2 implemented a way to run the Dada2 denoising algorithm by enforcing monotonicity? As the alternatives all point to R. Lastly would there be a possibility to add a note to the tutorials which include Dada2 in their analyses, to state that this is incompatible with binned quality scores (or specifically NovaSeq)?
Thank you for the continued great work with Qiime2!
Kind regards,
Johann