What can I do with an assembled genome? that is the main question I want to know.
A little more detail:
Before I have experience with RNAseq alignment, and now I'm learning genome assembly. Currently I am learning SOAPdenovo for assembly, and Valvet and MetaValvet afterwards. The question is: sure, I got a genome assembled, and let's assume I am satisfied with the gap-closing process and the final assembly. What's next?
I read that you can do genome annotation, and gene prediction. Anything else?
A little side-track: What would be a good tool to use for annotation and gene prediction?
Thanks in advance!