Parameter tuning to assemble chromosomal translocations

[AndreaGuarracino]

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?

[chhylp123]

Is it possible that you can share one sample that hifiasm is worse than verkko with me? I can have a look and figure out what happened.