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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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maybe mis-assembly of long tandem repeats #285

Open zhangrengang opened 2 years ago

zhangrengang commented 2 years ago

Here is an example: 360截图170810316377110

The coverage depths of A, B, B' and C are even, so the structure is expected to be A-B-B'-C or A-B'-B-C where B and B' is heterozygous tandem repeat units (~200 kb, de=~0.001 by minimap2) and A and C is their flank sequences. But hifiasm outputs two contigs A-B-C (linear) and B' (circular) instead of A-B-B'-C. I think A-B-B'-C may be better as it is more continous and more real.

chhylp123 commented 2 years ago

I see, thanks a lot. The UL-integration should be able to deal with this case reliably.