I have just completed some 16S sequencing on a large collection of samples, and as part pf this run I also included the Zymo Mock community.
However, I'm not really sure how to include the mock community into the analysis pipeline. Do I just classify the reads and look at the relative abundances compared to the expected abundances from Zymo and use that as an indicator to what bacteria may be over or under represented?
Or can it actually be used directly in the analysis pipeline? I'm not really sure where to start.