How to incorporate mock community into my analysis

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.

Good luck!

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