question about mapping parameters

[MaoYafei]

Hi,

I am trying to align a high-divergent hifiasm contigs to hg38 (divergent ~36 MYA, the SNV divergence ~10%).

I first tried the parameters (--eqx -ax asm20 --secondary=no -z 10000,50 -r 50000 --end-bonus=100 -O 5,56 -E 4,1 -B 5), then, I could get highly continuous mapped segments (please see P1.pdf the red blocks, please ignore the blue blocks(it is another assembly))). [P1.pdf]

As you see, there are lots of segments/sequencing are missing on chrX, chr16, and chr19 (p arm).

Then, I tried the parameters (--eqx -ax asm20 --secondary=no) and I could more fragmental mapped segments (Please see P2.pdf the red blocks. the three layers for segments >50kb, >10kp,<10kbp) []

As you see, I could align the 'missing sequences' to hg38, but I can not get larger contiguous aligned segments. [P2.pdf]

Then, I have couple questions about my mapping strategy:

1. Why are there so many sequences missing with parameters (--eqx -ax asm20 --secondary=no -z 10000,50 -r 50000 --end-bonus=100 -O 5,56 -E 4,1 -B 5) compare to the parameters (--eqx -ax asm20 --secondary=no )?

2. Could you recommend to me which parameters I should use to get more contiguous and 'no missing aligned segments?

Thank you in advance.

--Yafei