min ul length and inverted region

[EugeneKim76]

Dear all
I assembled genome using command shown below, then aligned assemblies to the reference.

hifiasm -o out.asm -s 0.55 -l3 --hom-cov 30 -k 30 --ul 40kb.fq --primary HiFi.gz
hifiasm -o out.asm -s 0.55 -l3 --hom-cov 30 -k 30 --ul 25kb.fq --primary HiFi.gz

(25kb.fq : Filter on a minimum read length 25kb, 40kb.fq : Filter on a minimum read length 40kb)

However, I found strange results shown below.
Is there any way to know which result is correct?

Best,

[chhylp123]

This is hard to say. It really depends on the reference genome you are using.