Does anyone have experience with whole gene sequencing?

I have been working with the phylos cannabis dataset (https://www.ncbi.nlm.nih.gov/protein/?term=cannabis+sativa )

I have downloaded the 2k or so varieties and am working with a Biochemist friend to create a data model. My hope is to start working with a home whole plant genome marker assisted breeding project. Im looking at the MinION (https://nanoporetech.com/products/minion) to sequence tissue cultured seedlings and my goal is to find similiar markers in an open breeding. I have some OGKush seeds I've been wanting to explore.

My question is. Has anyone done anything like this? I am stuggling with understanding the sequence comparisons and data model.

I appreciate the positive community and knowledge around here.