Q: Detection SV by aligning to diploid (not haplotype resolved) genome

[Alteroldis]

Dear Dr Chen.

I work with species, genome of which has a high number of genome rearrangements. Because of that I can assembly only diploid version of genome with Flye. And I think, I can resolve these by breaking my reads at points of structural variations and assembly them again. Will you approach work if I align reads to diploid genome, not haploid? And may be this resolve contigs of genome to different alleles (haplotypes)? Could I retrieve points of SV within of my reads from output of your tool?