What's next after Genome Assembly?

[polmed]

Hi,

This is a broader scope question rather than specific details.

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? What would be a good tool to use for annotation and gene prediction?

Thanks in advance!

[GenoMax]

If these are bacterial genomes then Prokka has been recommended by others on the forum for annotation. If you intend to make the genomes publicly available then NCBI's prokaryotic annotation pipeline may be of interest (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/).