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Published 20 hours ago • verified publisher icon chhylp123

Parameter tuning to assemble chromosomal translocations

Open AndreaGuarracino opened this issue 10 months ago • 1 comments

Hi, I have HiFi+ONT+HiC data for several samples carrying chromosomal translocations. For a few samples hifiasm does not catch the translocations, cases that verkko is able to resolve.

I tried:

  • hifiasm with default values with HiFi + ONT>=50kbps
  • hifiasm with default values with HiFi + ONT (all the reads) + HiC
  • hifiasm with default values with HiFi + ONT>=50kbps + HiC

What parameters of hifiasm can I tune, and how should I tune them, to make it more permissive/sensitive regarding resolving chromosomal translocations?

AndreaGuarracino avatar Aug 25 '23 14:08 AndreaGuarracino