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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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Recreate p_ctg from p_utg #653

Open diego-rt opened 2 months ago

diego-rt commented 2 months ago

Hello,

I'm trying to curate the assembly produced by hifiasm by reassembling the reads at the assembly tips with different parameters and assemblers. This would be bit more efficient if I could edit the assembly graph (manually add/remove or update nodes and edges), and recreate the contigs as hifiasm(UL) does. Do you by any chance have any code that you could share that could take the p_utg from the UL pipeline as input and output the primary p_ctg/hap1/hap2 graphs?

Thank you so much in advance!

diego-rt commented 1 month ago

@chhylp123 @lh3 Or alternatively, if hifiasm could output the order, orientation and coordinates of the unitigs used to generate each contig/haplotig, it would be super helpful for curation. In other words, similar to the 'A' lines in the current GFA but with unitigs rather than reads.

Thanks a lot in advance and sorry for the shameless feature request...

chhylp123 commented 1 month ago

@diego-rt Sorry for the late reply since I was quite busy this month. I will add this very soon.

diego-rt commented 1 month ago

Amazing, thank you so much @chhylp123 !!