I’d like to know if the MiSeq SOP contains the newest/best practices for 16S amplicon analysis? I’m working with V3V4 region MiSeq data. I currently have an older pipeline based on mothur, which as far as I can tell, works okay. I’d like to do a comparison with the latest mothur methodology to see if there is anything I need to change/update. I know mothur is flexible and there many ways to perform an analysis, but I just want to have a broad overview of the newest workflow and if it’s actually better than what I have.