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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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--dual-scaf #599

Open tallnuttrbgv opened 7 months ago

tallnuttrbgv commented 7 months ago

Hi,

can you please describe the options '--dual-scaf' an d'--scaf-gap'. There is no description of it in the documentation. Is this for Hi-C scaffolding or ONT?

Thanks,

Theo

tallnuttrbgv commented 2 months ago

Hi,

in the latest version there is still no explanation of this option in the manual, help, or tutorial. Can you please provide a brief explanation?

Thanks,

Theo

chhylp123 commented 2 months ago

Sorry for the late reply since I was quite busy this month. Basically, '--dual-scaf' is designed to execute dual scaffolding without needing additional data. Essentially, the two haplotypes scaffold each other. The process mirrors two rounds of reference-guide scaffolding: initially, haplotype 1 is scaffolded using haplotype 2 as the reference genome, and then vice versa. '--scaf-gap INT' is used to make sure that the assembly gap won't be too large. In some cases like centromeres, two haplotypes might be significantly different in length. This is why the default value for '--scaf-gap INT' is 3M. I will add update tutorial soon.