<p>Hi all,</p>

<p>Our lab has sequenced 20 different strains of the same bacterial species.  I now want to analyse these data, i.e., link genomic data to virulence (some of the strains are virulent, others aren't) and other phenotype differences.</p>

<p>I started with de novo assemblies and mapping to an annotated reference genome.  However, it is unclear to me how to proceed now in a good way.  Most of the information for comparative genomics I find on the web applies only to the human genome or one-to-one comparisons of bacterial genomes.</p>

<p>Is there a standard workflow for this kind of analysis?  Does anybody know of any good tutorials/references/articles?  How would you proceed?</p>

Part of my thesis was on comparative genomics to get closer to uncovering the genomic basis of virulence in *Neisseria meningitidis*. I think that two good papers to look at are [Schoen et al 2008][1] and my own paper [Katz et al 2011][2].  

Schoen compared genomes on the gene level; my group looked for SNP-level differences.  For the genome project part of it, ie assembly-to-annotation, we used [CG-Pipeline][3].  However, a more interactive service like [RAST][4] or [BASys][5] might be easier (although less comprehensive in annotations). NCBI's PGAAP annotations however would make it easiest to submit the genomes to NCBI at the end of the study.

Anyway, I think that the methods in Schoen et al and Katz et al would be very relevant to your questions.

 [1]: http://www.pnas.org/content/105/9/3473.full.pdf
 [2]: http://jb.asm.org/content/193/14/3633.short
 [3]: http://sourceforge.net/projects/cg-pipeline/
 [4]: http://rast.nmpdr.org/
 [5]: http://basys.ca/basys/cgi/submit.pl