Merge.otus and representative sequences

Hello, is there a way to run merge.otus on uniques and then get representative sequences from get.oturep and create.database?

Sorry, merge.otus is really meant to merge the counts of OTUs that have the same taxonomy.

Do you mean to do this at the level of ASVs? If so, you can run the sequence and count data into make.shared as explained for ASVs in the SOP to generate a list file

I’ve classified uniques with make.shared and then merged strains with the same taxonomy to be able to whittle down the number of OTU and run statistics.

For my study organism, this approach can shift ~2000 unique OTU into ~120 which allows me to run some statistical tests. If I create ASVs, won’t I need to do a similar step to merge them into the same taxonomy?

Sorry, I’m not really following what you did. make.shared is for creating a shared file, not for classifying sequences.