Designing a lab NGS file database schema
The Global Alliance for Genomics and Health has been working on the issue of representing sequencing data and metadata for storage and sharing for quite some time, though with mixed results.  They do offer a model and API for storing NGS data in their GitHub repository, but it can be a bit of a pain to get a high-level view.  I am not sure if any better representation of this exists elsewhere.

I can say from personal experience (having built over a dozen genomic databases), there is no ideal data model and storage best practices.  Genomic data comes in many shapes and sizes, and your needs are going to vary from every other organization, so what works for one bioinformatics group won't necessarily work for you.  The best thing to do is design and implement a model that will cover all of the data types in your workflow and downstream analyses you might do with the data and metadata.