How to identify the SV between two genomes from two species

[aaannaw]

hello，Professor
I have two genome from two species and　two set of hic reads from two genomes. I want to identify SVs between two genomes from two species by hic reads. I am confused whether should I align B genome hic reads to A reference genome to generate the input cool file of EagleC？
Could you give me any suggestions?
Looking forward with your reply!

[XiaoTaoWang]

Hi, thanks for your interest ... but EagleC was not designed for identifying SVs between genomes of two species. Actually, since the sequences of the two genomes are known, I think the most straightforward way for your task is to align the two genomes using a traditional sequence alignment software :)