Denovo sequencing on known reference

[foxyg]

I remember reading a paper talking about how denovo sequencing is useful even on known reference. Because each people's genome is slightly different. I am trying to find that paper again but couldn't anymore.

I have some exome sequencing illumina data, I am wondering if it is worth it to do denovo sequencing in this case.

What is your take on this subject?

Thanks

[v_kisand]

I guess you mean human genome... well I work with almost exclusively with bacteria but I do not see any advantage in de novo sequencing over reference mapping. you have to be really sure that you expect substantial re-arragements in genome of interest. Which might be easily case with various strains of bacteria ... in human genomes, I am not expert on this field but I doubt...

Originally Posted by foxyg

I remember reading a paper talking about how denovo sequencing is useful even on known reference. Because each people's genome is slightly different. I am trying to find that paper again but couldn't anymore.

I have some exome sequencing illumina data, I am wondering if it is worth it to do denovo sequencing in this case.

What is your take on this subject?

Thanks

[krobison]

There are regions of structural variation which are not captured in the reference genome for any species.

One approach is to first do reference mapping, then assemble what doesn't map. Similarly, localized assembly of regions you know are dodgy -- such as if a high frequency of only one side of a paired end read mapping next to that region.