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zengxiaofei / HapHiC

HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data
https://www.nature.com/articles/s41477-024-01755-3
BSD 3-Clause "New" or "Revised" License
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Assemble a diploid genome based on Hi-C data from a tetraploid genome assembly #50

Closed awesomedeer closed 2 months ago

awesomedeer commented 3 months ago

Dear Zeng @zengxiaofei I have a chromosome-level tetraploid genome assembly which was scaffolded by Hi-C results. I found in pulic data that a diploid individual was sequenced by long-reads sequencing but lack of Hi-C data. Since I have seen the powerful scaffolding by HapHiC, I was wondering if I can use the Hi-C data from another study to scaffold a diploid genome by reducing the parameters through mapping the HiC reads. etc? Although i's a bit beyond the purpose of this software, I bet you might have some good ideas!

Best regards Song

zengxiaofei commented 3 months ago

If this diploid assembly is not haplotype-resolved (i.e., haplotype-collapsed or primary), it is acceptable to use Hi-C data from other individuals to scaffold this assembly. This approach is very similar to reference genome-based scaffolding. However, the results should be interpreted with caution.

zengxiaofei commented 2 months ago

Close this issue as there has been no response for two weeks.