To decrease per-sample sequencing costs in some large studies, our data was produced in a NovaSeq instrument. When we started working through the datasets our quality plots looked very odd, which led us to identify the new quality binning as the cause. (thanks to some posts here!!)
The question is: are there any best practices for working with this data? We are concerned that using any algorithm that takes into account quality scores is no longer appropriate, however, we are at an impasse regarding what the best approach is.
Use Dada2 R package with modifications as described by the link.
Use Dada2 R or q2-Dada2 as it is, since there are several reports with not significant variations between using Dada2 as it is (R or Qiime2) and modified version
Use Deblur which is not affected by changes in quality scores bining.