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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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Generating arbitrary pseudohaplotypes #90

Closed skagawa2 closed 2 years ago

skagawa2 commented 2 years ago

What is the best way to generate hifiasm-like primary contigs from the results of verkko? For reference, we generated an assembly with only HiFi reads because we don't have ONT reads. I saw #59 and I ran purge_dups, but I'm not completely sure how that will stitch together haplotype blocks into a primary assembly. For our project, we don't need a completely phased assembly since we don't have phasing information.

Thanks!

skoren commented 2 years ago

Verkko doesn't currently have a way to pull out pseudo-haplotypes. The only option would be if you were to generate these paths from the graph yourself. That said, verkko isn't designed for your specific use case, HiFi-only and no long-range phasing information. It does best with the long-range ONT information plus trio or hi-c or other phasing info.

skagawa2 commented 2 years ago

Makes sense. Thank you for your quick reply!