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rlorigro / GFAse

Tool for globally phasing diploid assembly graphs with orthogonal data
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GFAse on Hifiasm assembly #18

Closed nirvana693 closed 1 year ago

nirvana693 commented 1 year ago

Hi

In case I want to use GFAse on hifiasm assembly, which is recommended to use haplotype-resolved raw unitig graph (r_utg.gfa) or the processed one (p_utg.gfa)?

Is it possible to use parental data on Hifiasm? (based on preprint No)

Thank you

rlorigro commented 1 year ago

Hi,

The recommended GFA is the p_utg GFA, which has the bubbles popped already. However, Since Hifiasm has an unresolved issue of broken overlaps in the GFA, you can only expect to assign the contigs to maternal/paternal bins, and not extend/chain them.

Parental illumina data would be better off just running trio-hifiasm, and if you have illumina Hi-C it would probably also be better to run the hifiasm hi-c module.

nirvana693 commented 1 year ago

@rlorigro Thank you