How computationnaly verify a right ordering and orientation of a part of genome sequence with short reads illumina data

Question

[angez9914]

Hello everyone!

The whole genome alignment of a reference genome A (constructed with short reads + genetic linkage map) with a new genome B (short reads + pacbio long reads + Hi-C) revealed some inversion patterns in some chromosomes suggesting ordering and/or orientation problems. How can I elucidate the right ordering and orientation of the inverted region using short reads data? I want to know between A and B, which genome has the right orientation. Sincerely Yours.