Roye Rozov asked -
We looked for answers at various places and found the following application notes posted by @coxtonyj useful (click on figure to download pdf file) -
Regarding assembly strategy, Dr. Cox told me -
Parsimonious adapter trim then Velvet, making best use of lesser-known Velvet options. Hope to release as BaseSpace app soon.
Readers curious about relative performance of Velvet vs other assemblers will find the benchmarking table at the SPAdes website helpful. SPAdes group also releases their assembler as an app in BaseSpace.
Others with more direct experience with the topic please chime in.