ONT data model result.

[zhidaobuzhidao]

Hello,
I have tested the ONT assembly mode you recently released using the UL ONT data. The result is a little strange.

The genomic material size is approximately 470M. The result genome size in hifi (180X) +UL ont (120X) mode is close to the estimate,~470M.
Only using UL ONT data in the ONT mode (--ont), the assembly size is only 14M. The kmer peak map of the data in the log has no peaks and no homologous peaks can be found.

What might be the reason for this? What other attempts can we make?

Best regards,
Ben

[chhylp123]

Even though the ONT reads have higher error rate, it should still be able to find peaks. Are you using R10 data?

[zhidaobuzhidao]

Unfortunately, I just confirmed that this test data is not R10, but for the R9 chip.

[chhylp123]

Then hifiasm currently wouldn't work well for the old R9 data.

[zhidaobuzhidao]

Thank you for your reply. We look forward to even better performance from hifiasm

[wangzhaohui-001]

Unfortunately, I just confirmed that this test data is not R10, but for the R9 chip.
how to check ul data is R10 or R9?

[chhylp123]

I fee like most ONT reads produced after 2023 should be R10.