Newest/best practices for mothur

Hi all,

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.



Hi, the MiSeq SOP reflects the latest/best practices. We still consider V3V4 and the v3 chemistry to be a poor choice for analyzing data. Every piece of data we’ve seen and worked with indicates that to get good denoising, you need to have fully overlapping reads. This blog post still describes our experiences with the v3 chemistry.