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tangerzhang / ALLHiC

ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
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How to anchor two haplotypes of simple diploid genome? #99

Closed xiekunwhy closed 3 years ago

xiekunwhy commented 3 years ago

Hi,

I got 2 haplotypes of a simple genome using hifiasm(https://github.com/chhylp123/hifiasm) with HiC data, and I want to know how to anchor these two haplotypes to chromosome-level using allhic. 1) To anchor them separately or 2) cat them together and anchor them to 2n chromomes?

Best, Kun

tangerzhang commented 3 years ago

Anchoring them separately would be much easier than the second approach.

olekto commented 3 years ago

I'm sorry for replying to a closed thread, but I basically have the question and would like to ask a couple of follow-up questions.

Sometimes, the two haplotypes might have large differences, inversions for instance, where actually splitting the HiC data in some way into the two haplotypes would be beneficial. If one concatenates the two haplotypes, and then map HiC reads to the diploid (or dual) assembly, then some HiC reads would map to each haplotype, but maybe not enough for scaffolding? With more and more assemblers outputting diploid or dual assemblies, it would be nice to have a haplotype-aware way of scaffolding them.