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pangenome / pggb

the pangenome graph builder
https://doi.org/10.1038/s41592-024-02430-3
MIT License
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How to deal with dual assembly [question] #161

Closed baozg closed 2 years ago

baozg commented 2 years ago

Hi,

Chromosome-scale phasing need another data type. The hifiasm HiC phasing paper introduce a new mode for assembly (http://lh3.github.io/2021/10/10/introducing-dual-assembly)?
Can we use dual assembly with haplotype? Scaffold hap1 and hap2 with synteny and follow the PanSN-spec to build pangenome graph. Did it vaild any assumption of pggb or vg ?

Thanks.

subwaystation commented 2 years ago

Hi @baozg,

I don't think there will be issues regarding the naming scheme. In principle, having a true phased assembly or a dual assembly, the naming scheme seems to be the same. So I would not expect any additional issues using dual assemblies.

Best, Simon

baozg commented 2 years ago

Thanks for reply.