Dear Falk,
I am dealing with an ITS dataset (earth microbiome amplification protocol) and I have tried dada2 (roughly 50% of ASVs unclasified at phylum level), usearch (the same for otus or zotus), but when using lotus I found that 85% of otus were classified at phylum level.
I wonder if there is a plan to allow lotus to use usearch/uparse zotus in the following updates. I had to move to ASVs because reviewers asked me to do that.
Regards,
Manuel