tiro binning need the comform parantal trio data?

[Mengjuan11]

Hello, professor I want to know the differences bewteen trio modle and HiC model? Is there a difference in the detection of structural variation? Will the trio model completely split the genome into two sets, ignoring the crossover and rearrangement of chromosomes? The second issue: For the trio model assembly, the required parental illumina data must be clear which variety or just the reference genome species can be well phased?

[chhylp123]

I want to know the differences bewteen trio modle and HiC model?

If you have trio, it would be better to use trio as trio-binning is more clear.

For the trio model assembly, the required parental illumina data must be clear which variety or just the reference genome species can be well phased?

You should use the short reads from the parents.

[Mengjuan11]

thank you very much for your reply. For our plant, we do not confirm which variety the parents is, just know it was hybrided with two specise. And now we have short reads of these two species(one is wild reference species ). Can we use the trio-hifi method？

[chhylp123]

I guess Hi-C should be more safe.

[Mengjuan11]

Hello, professor Because our species is a diploid of interspecific hybridization, it is not clear whether the recombination and exchange between the two sets of chromosomes have occurred. I want to retain this structural variation, so I would like to ask the professor whether the trio-binning typing is directly excluded the chromosomal rearrangement, resulting in undetectable chromosomal rearrangement variants?