hom-cov option

[plant-assembler12]

Hello,

First of all, I would like to thank you for developing such a great program.
I am assembling a 450 Mb plant genome using hifiasm.
This plant is diploid with very low heterozygosity and very high homozygosity.

Initially, when assembling with the default options, I noticed that hap1 and hap2 were smaller than the primary assembly. Therefore, I decided to adjust the --hom-cov option. Below are the sizes of the primary, hap1, and hap2 assemblies for different values of --hom-cov.

To me, hom-cov 120 seems the most ideal. However, the hifiasm log indicates that the homozygous peak is at 167
, while Genomescope suggests the peak is at 113.
Thus, while choosing 120 yields better results, it seems to lack a strong basis based on k-mer peaks.
plasnt_hifiasm_default_option.log

Does it make sense to use --hom-cov 120? Could changing the --hom-cov option lead to incorrect assembly of the genome?

[chhylp123]

You may check the FAQ here: https://hifiasm.readthedocs.io/en/latest/faq.html#how-can-i-tweak-parameters-to-improve-hi-c-integrated-assembly. If the BUSCO score is not bad, probably --hom-cov 120 makes sense.

[plant-assembler12]

Thank you for your kind response. The BUSCO value currently seems fine. I will proceed with scaffolding after checking the QV. Have a great day!