How to split HiC reads into haplotypes?

phasegenomics / FALCON-Phase

FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds

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Open DayTimeMouse opened 1 month ago

DayTimeMouse commented 1 month ago

Hi，

Thanks for developing this nice tool.

I have obtained two haplotypes assembly(hap1.fa and hap2.fa). Then, how to get haplotype-specific HiC reads? Using haplotype-specific kmers?

Can FALCON-Phase do this? Or, do you have some ideas for this?

Best regards.