Hi @hulfred,
I don’t believe an independent benchmark has been performed yet to help inform a decision here. The algorithms do have similarities, and key differences. And to be transparent, I am a developer with Deblur.
At a high level, DADA2 uses PHRED scores to inform an error model. Deblur deviates from this and instead uses a static error model. As a result, DADA2 is potentially better able to accommodate run specific errors. The benefit of a static error model though is that it potentially reduces study bias; the use of a static model was an important criteria for Qiita, the American Gut Project and the Earth Microbiome Project as these efforts are focused around meta-analysis.
@benjjneb, do you agree? I apologize in advance if I made a mischaracterization.
Best,
Daniel