I thought this was considered impossible, but now someone did it:
Very frustrating. The press release offers no clue at all as to how they manage to assemble the separate chromosomes.
I found the original paper here: https://www.nature.com/articles/s41467-020-15848-y
Not sure whether it is freely-accessible or whether I just happened to have access through my university. In brief, they use a “trio” method for resolution of haplotypes that involved not only long reads from the hybrid, but short-read sequencing of the putative parents as well.
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Thanks. This would appear to be the actual methods paper:
Koren, S. et al. De novo assembly of haplotype-resolved genomes with trio binning. Nat. Biotechnol. 36 , 1174–1182 (2018). Unlike the other paper, it’s paywalled.
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You do need some sequences from the parent individuals or the parent species. We should have realized that. If, by computational magic of some sort, you manage to get for a pair of chromosomes fully resolved phased genomes all along the chromosome, then you still can’t tell which came from which parent. Unless you have some sequences from the parents.
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