LOL. Who said that? Did they show any actual data? Reviewers who trash manuscript for using mothur over QIIME or QIIME over mothur are lazy and don’t deserve to review manuscripts. They need to provide specific points for why one should be used over the other.
For instance, I would have serious problems with papers that use open or closed reference clustering in QIIME based on the series of papers we have published over the past few years.
I would also have problems with people using ASVs and rejecting OTUs out of hand. ASVs have a real risk of splitting 16S rRNA genes from the same genome into different ASVs. When you add that dada fits a model with hundreds of parameters and then applies a ridiculously low p-value threshold, you start to see that it has problems. The reality is that dada looks better than mothur’s pre.cluster because they remove all of the singletons. If you leave them in, the performances are about the same. Removing singletons will have a negative impact on the ability to calculate alpha and beta diversity metrics and estimate relative abundance.
You might also want to read a lengthy blog post I wrote on mothur and QIIIME.