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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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Duplicated BUSCO for polyploid genome #581

Open Phytoecia opened 8 months ago

Phytoecia commented 8 months ago

Hello,

I am using hifiasm to perform hifi-only assembly of a allopolyploid species. While the basic metrics are good (high N50, Complete BUSCO>98%), I got only 57% of Duplicated BUSCO. I suspected the homoelogues have been merged at some point in our run. In the Hifiasm paper, the strawberry genome showed very high Duicated BUSCO, which we desire. What can we try more?

Best, Minsoo

chhylp123 commented 8 months ago

I suspect a lower BUSCO score might be better?

Phytoecia commented 8 months ago

Actually higher duplicated BUSCO score is expected as our model species has allotetraploid genome. I found that the p_utg file shows duplicated BUSCO>95% while the p_ctg file shows 57%. It seems that the purging step removes duplicated genes (which should remain). Thank you!

mirkocelii commented 7 months ago

If hap1 and hap2 are both duplicated, it must be a real tetraploid