Hello!
Did you already find this issue on the Dada2 github? https://github.com/benjjneb/dada2/issues/791
So, options are:
- 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.