Designing a lab NGS file database schema I am the resident Bioinfo Geek in a hospital academic lab that routinely employs NGS as well as CyTOF and other large volume data producing technologies. I am sick of our current "protocol" for metadata collection and association with the final products (miriad excel sheets and a couple poorly designed RedCap DBs).

I want to implement a central structured, controlled datastore that will take care of this. I know that the interface to the technicians how will be inputing the data is crucial to its adoption, but this is not the focus of THIS particular question: Does there exist a schema or schema guidelines for this type of database?

I would rather use a model that has been developed by people who know how to do this well. I know of BioSQL but it seems more geared towards full protein/nucleotide records like those found in uniprot or genbank. That is not what we have here. What I want is something similar to the system touched on in this preprint: http://biorxiv.org/content/early/2017/05/10/136358

Alternatively, can anyone provide links to where I might find relevant guidelines or supply personal advice?
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.