Hi @AnkeWigger,
Thanks for reaching out! Happy to provide some suggestions below:
As discussed in this forum post, you have a few options here:
- Use the dada2 R package with modifications as described by the Github link you shared above.
- Use the dada2 R package or q2-dada2 as it is, since there are several reports without any significant variations between using Dada2 as it is (R or Qiime2) and the modified version.
- Use Deblur which is not affected by changes in quality score binning.
Hopefully one of these options is a good solution for you!
Cheers :qiime2: