Switch error on X and Y chromosome

[Lin-Yuying]

Hi Haoyu,

Thank you so much for developing this amazing tool that enables the haplotype-resolved genome assembly.

Previous studies show that hifiasm can successfully seperate X and Y contigs into two haplotypes. However, since there are pseduautosomal regions (PAR) on the X and Y share homologous sequences, it is possible that there are switch errors when phasing X and Y contigs. In this case, how should I evaluate the switch error rates between the X and Y contigs in two haplotypes?

Thanks you so much in advances!

Best,
Lin

[chhylp123]

Hi @Lin-Yuying , sorry for the late reply. Trio-binning assembly should be fine in most. Without parental data, Hi-C contact or reference-guided curation might work.

[Lin-Yuying]

Hi Haoyu,

Thank you so much for your reply and sorry for being confusing in the original post.

I did run Hifiasm with HiC mode, and except this, I am wondering if there is a seperate way that I can identify the switch errors from two assembled haplotypes, especially the sex chromsome regions.

Best,
Lin