bionano hybrid scaffold

Question

[lait]

Hi,

is it possible to use illumina whole exome sequencing data as input for the hybrid scaffold tool in bionano access software ?

I have WES data and bionano assembly data for the same sample. I was wondering if the WES data is enough to be used by the hybrid scaffold tool?

Thanks

[Friederike]

Do you have a link to the documentation of the Hybrid Scaffold Tool in the Bionano Access Software? Why do you think that WES data might be appropriate input for that?

Answer 1

[WouterDeCoster]

Whole exome sequencing is not continuous and has large gaps. Your assembly will be terrible. It may work, but it is pointless.

[lait]

thanks for your answer, that is correct. but do you think WES data could be in any way useful , as a complementary data, for the bionano optical mapping?

[WouterDeCoster]

Oh certainly. You could use the WES for calling SNVs in the exons, and you could use the bionano data to identify larger structural variants.