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.
Quality control is one piece you could incorporate into your workflow, as documented here.
It becomes relevant after you have processed your samples (imported data, trimmed reads, denoised, etc.).
see this tutorial for an example of using q2-quality-control in a complete workflow: Fungal ITS analysis tutorial
it has an example of expected compositions (as a TSV) and how they are imported to QIIME 2.
See also that tutorial — the observed composition is your feature table collapsed on taxonomy (at the same rank as your expected taxonomies) and then converted to relative frequency.