Next Generation Sequencing (NGS) technologies dropped down sequencing costs and times for obtaining data. Now it is almost easy to obtain the complete genome of an organism of interest (faster if re-sequencing). Comparative genomics could then highlight features making our strain of special interest. How affordable is it to apply this vision at large scale through public health microbiology units? Do public health systems working in such a way exist?
thank you for the reference, I am figuring out (by shotgun simulations) how much we can push down genome coverage to reach the minimal sequencing effort to have enough information and pooling more genomes in one experiment using MIDs. Here the problem is that each library will rise the price per genome.
Another issue is how to find an useful tool to analyze these kind of huge data. Does anyone have any suggestion on this issue?
Well, there are several software now that can do, for example, mapping or SNPs searches. Pipeline are then mounted to automatize processes. Servers and clusters are nowadays powerful enough to cope with the work. We already work with comparative analysis of many genomes at one time. The main effort, in my opinion, is the translation from experimental world to public-health world.
Hi, whole genomes of bacteria from Human Microbiome can be useful for understanding their role in human health. There must be some genomic signatures for their symbiosis and survival in human system. But sequencing whole microbiome for each individual is still beyond the affordability.
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