What are example use cases?

[ahwagner]

The docs (from what I could find) do not provide common scenarios where collections are useful. This is probably self-evident to the team. However, for people that have less clear notions about how this might be used, it would be good to see some examples of the specification as intended by the developing team.

Am I missing this, or is this just yet to be documented?

[nsheff]

Use cases or "user stories" are documented in this google doc.

We should probably pull some of these out into the docs.

[nsheff]

Just following up on this, @ahwagner did you find that document useful? Do you think it's worth the effort to pull those stories out and put into the seqcol website?

[ahwagner]

I think it would be helpful to highlight how SeqCol solves a common problem. I am more familiar with the spec now than I was 9 months ago. The user stories in that document (most of which are covered by SeqCol) get at useful functions of the specification. However, I think what really needs to happen is to put the most common envisioned use case (in a concrete scenario) front and center in the RTD site.

For example, you may describe a story of adding a SeqCol identifier to a SAM header, and using that to validate that alignments refer to the same underlying genomic reference sequence set. Perhaps make the example a little more complex, and show how a group may include decoy sequences to remove contaminant sequence, and as those decoys and or reference contigs are updated over time the corresponding sequence collection identifiers remain compactly stored within the alignment file headers for quick and easy validation between alignment files.

You may then describe how this is a better situation than simply using the existing @SQ header lines, e.g. how this enables the SeqCol comparison operations. Perhaps this is already part of the planned text under "More details to be added here later." on the landing page?

That said, this might not be a problem for the average user that finds their way to the SeqCol RTD.