continuous on the unitig graph but breaked after Hi-C resolving

[zhangrengang]

The below is an example: the two chromosome-level haplotypes are continuous on the unitig graph, but in the final hic.p_ctg, one unitig (charactered as “A”) is breaked. The black lines indicate correspondences between unitigs and HiC-resolved contigs.

[chhylp123]

Do you mean it is a misassembly or unexpected breakpoints?

[zhangrengang]

It should be an unexpected breakpoint, as it is connected on the unitig graph and neighboured on the Hi-C heatmap.

[zhangrengang]

The breakpoint is absent with another HiC dataset by a different enzyme.