Two assemblies

You have an alignment of one assembly against another, in PAF, as minimap2 writes it.

karyon asm1_chr1 assemblies.paf -o assemblies.svg

The place is the sequence of the first assembly, as the PAF names it. The ribbons join each stretch to where it aligns in the second assembly, and the key says which colour is the same strand and which is reversed.

Change it

To	Write
Draw it as a dot plot	--dotplot assemblies.paf
Zoom into one stretch	asm1_chr1:100,000-300,000 in place of asm1_chr1
Make the PAF	minimap2 -x asm5 first.fa second.fa > assemblies.paf

The example file: assemblies.paf. Every option: karyon help synteny, or the command line reference.