I wonder if we can do comparative genomics using draft genomes from shotgun sequencing. I mean, since there might be uncharacterized genes or proteins because they are located in the gap between the contigs, will it still be "valid"? Do you think we will get much less information if we do comparative genomics using contigs or scaffolds from shotgun sequencing compared to the whole genome for bacteria?
If contigs or scaffolds are still OK, what kind of analyses can we perform?
Thank you for any input here.