First appearing in the 2025.10 version of QIIME2, there are important changes to the DADA2 plugin. Two parameters available in the R version of DADA2 that greatly simplify correctly processing variable length amplicon data have been exposed. One is the capability of trimming overhangs using –p-trim-overhangs. The second, the –p-max-merge-mismatch parameter, allows mismatches in the overlap region when merging pairs. By default, DADA2 allows no mismatches in the overlap region, but with variable length amplicons when the overlap length can exceed 100 bp this is simply too strict.
There is also a new mandatory output, the base-transition-stats. Output as a qza file, they can be exported as large tsv file, but to make the stats more easily interpretable I have added the function plot_transition_stats() to QsRutils. The objective is to check how well DADA2 is modeling transition errors and correcting sequences before merging them. As an example:
QsRutils::plot_transition_stats(base-transition-stats.qza)