Annotation of multiple bacterial genomes

[lizzi]

Hi,
I would like to annotate a subset of the Human Microbiome Project Reference Database http://www.hmpdacc.org/HMREFG/
and am wondering if anyone has any advice as to the best (and reasonably fast) system to use for annotating multiple bacterial genomes. There are just over 2000 FASTA sequences (~2.3 Gb) - some are complete genomes, and some are scaffolds.

Thanks!

[TiborNagy]

RAST is an online tool for bacterial genome annotation.
PROKKA also a great tool.