make 'salmon' or 'quantify' an equal citizen

[ctb]

A common use case for transcriptomics doesn't involve de novo assembly, but rather just quantification or (perhaps) annotation + quantification, for semi-model organisms like dog and cat which have good reference genomes but not great transcript annotations.

While eelpond can probably handle both of these, the docs for e.g. salmon really focus on addressing the de novo transcriptome assembly case:

https://github.com/dib-lab/eelpond/blob/master/docs/salmon.md

but I think that eelpond could usefully serve the reference-based case as well.

[bluegenes]

As part of this, split the getting started or `quickstart into two sections:

• "Starting from reads"
• "Starting from an assembly"