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c-zhou / yahs

Yet another Hi-C scaffolding tool
MIT License
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Avoiding telomere false joins #32

Open GwynHN opened 2 years ago

GwynHN commented 2 years ago

Hi,

I have assembled the highly heterozygous and repetitive genome of a plant using HiFi and Omni-C, running hifiasm to generate a phased diploid assembly. I then processed the omni-c reads through their suggested valid pair pipeline on just the hap1 assembly. Using that BAM (converted to BED) output, I scaffolded the hap1 assembly with YaHS using default settings. When I compare these scaffolds to those of a related species, it seems I got the rare case of telomere to telomere false joins for all of the scaffolds.

Is there anything I can do with the input or options to consider when running YaHS to reduce the possibility of these joins? Are you potentially trying to implement a way to avoid these types of joins?

Best, Gwyneth

c-zhou commented 2 years ago

Hi Gwyneth,

Sorry for the delayed reply. The current version does not have specific parameters to deal with this problem. We are currently working on this. Hopefully, it will be solved (to a certain extent) in the next version.

Best, Chenxi

amvarani commented 4 months ago

Hi @c-zhou

Any news regarding this issue ? I have the same problem here. Look below

image