references folder

[pschloss]

This looks great! I think it might be good to add a references or refs folder. For genomics/microbial ecology project we often use references to map our data against or for classifying sequences. We find it is helpful to have all of those references in a single place.

[hlapp]

You probably mean as a subfolder to data/, right? The term reference genome is very common in genomics, but I worry whether references is otherwise not easily confused with literature references. Is there another possibly more generic term that's less prone to confusion?