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dfguan / purge_dups

haplotypic duplication identification tool

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haplotype resolved assembly

m-jahani opened this issue · comments

commented

Hi,

I am working with HIFI+HiC haplotype resolved assembly with HIFIasm (both have been also scaffolded with HiC data). Based on BUSCO and Merqury results, assemblies contain ~%3-4 duplication. I want to run purge_dups to get the bed file for suspicious regions for false seg dups.
What's the best way to run purge_dups for each haplotype?

  1. Merge hap1 and hap2 and run purge_dups?
  2. Run purge_dups separately for each haplotype (the HIFI reads are the same for both haps)?

Thanks

commented

In other words, How can I find the coordinates of remaining false duplications in a haplotype resolved assembly?

commented

Hi~

I face the same problem just like yours,have you got the problem solved? Can you tell me your solution?

thank you so much