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marbl / verkko

Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.
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Producing dual assemblies when no trio or Hi-C data is available #157

Open smkumaill opened 1 year ago

smkumaill commented 1 year ago

When there is no trio data available, is it possible to produce hifiasm style pseudo-haplotype resolved assemblies?

I was not able to produce the pseudo-haplotypes from the final assembly. Do you have any suggestion as to what tool or method could be utilized to produce these pseudo-haplotypes (if at all possible).

skoren commented 1 year ago

There is currently no unphased output from verkko. However, the combination of hifi and ONT data produces much longer phase blocks than hifi alone (e.g. megabases vs kps on human). The size of the blocks will vary depending on the heterozygosity of the sample. I would suggest looking at the output graph to see how much connectivity remains in your sample due to large homozygous regions. If there are almost none, you can do a simple purge to get a single haplotype on the final assembly (using purge_dups). If not, the only current option would be to provide paths manually through the graph.

skoren commented 1 year ago

We've discussed producing a primary/alt style output so I've added the enhancement tag and will keep this open as part of future development.