Interchromosomal misjoin

[Han-Cao]

Hi,

I am using hifiasm 0.19.8-r603 to do human genome assembly using hifi-only data. After the assembly, I found there is a interchromosomam misjoin reported by paftools.js misjoin -c centromeres.bed -e align_to_chm13.paf.

To troubleshoot the assembly, I aligned the hifi reads to the assembly and check the misjoin position in IGV. In the IGV view, the left part of assembly was aligned to chr10, and the right part of the assembly was aligned to chrX.

Moreover, the region within the blue window has a lot of mismatches and double depth, does it mean that region is a fusion from 2 chromosomes? If I want to manually fix this issue, can I split the assembly into 2 regions: one end with the left blue line, another one start from the right blue line, and drop the region within the blue lines?

Thank you!