nucmer to identify large insertion/PAV for building linear pangenome

[yongjiam]

Hi,
I am looking for expertise suggestions to fine tune nucmer parameter for identifying large insertion and PAV between two large assembled genomes like barley (4.5 Gb, 7 chromosomes).

I am aiming to detect gene insertions (within a ~ 0.6 Mb fragment insertion) between 2 barley genome, like the one in Figure 1d in this paper:
https://onlinelibrary.wiley.com/doi/10.1111/pbi.14264

My current command testing different --maxgap are as below. I used show-coords to output the query alignment region, no run does seem to recover this 4 gene insertion, could anyone advise me how to modify the nucmer options to potentially recover this large insertion? Many thanks in advance.

I tested maxgap ranging from 1000 to 5000000, no run seems to work:

nucmer -b 1000 --maxgap 1000 --mincluster 10000 --diagdiff 50 --minmatch 200 p65_1H.fa p35_1H.fa --prefix 1H_1000
nucmer -b 1000 --maxgap 5000 --mincluster 10000 --diagdiff 50 --minmatch 200 p65_1H.fa p35_1H.fa --prefix 1H_5000
nucmer -b 1000 --maxgap 10000 --mincluster 10000 --diagdiff 50 --minmatch 200 p65_1H.fa p35_1H.fa --prefix 1H_10000
nucmer -b 1000 --maxgap 50000 --mincluster 10000 --diagdiff 50 --minmatch 200 p65_1H.fa p35_1H.fa --prefix 1H_50000
nucmer -b 1000 --maxgap 100000 --mincluster 10000 --diagdiff 50 --minmatch 200 p65_1H.fa p35_1H.fa --prefix 1H_100000
nucmer -b 1000 --maxgap 500000 --mincluster 10000 --diagdiff 50 --minmatch 200 p65_1H.fa p35_1H.fa --prefix 1H_500000
nucmer -b 1000 --maxgap 1000000 --mincluster 10000 --diagdiff 50 --minmatch 200 p65_1H.fa p35_1H.fa --prefix 1H_1000000
nucmer -b 1000 --maxgap 5000000 --mincluster 10000 --diagdiff 50 --minmatch 200 p65_1H.fa p35_1H.fa --prefix 1H_5000000

[Jnhcau]

Hello, have you found a good solution?