minimap2 -x asm does not detect some alignments / synteny

[theo-allnutt-bioinformatics]

Hi,

using a test file of three chloroplast genomes, attached, minimap2 fails to properly align all repeats - the inverted repeat of the genomes are not shown - see plots below.

brassica_chloroplast.fasta.txt

minimap2 -x asm20 -t 48 brassica_chloroplast.fasta brassica_chloroplast.fasta > brassica.paf
pafCoordsDotPlotly.R -i brassica.paf -o brassica -q 100 -m 100 -p 8 -l -x -k 3

but nucmer method looks ok:
nucmer --maxmatch -l 80 -c 100 brassica_chloroplast.fasta brassica_chloroplast.fasta -p brassica.nucmer
mummerCoordsDotPlotly.R -i brassica.delta.coords -o brassica.plot -x -m 100 -q 100 -k 3 -s -t -l -p 12

I am not sure if this is problem with dotPlotly or minimap2, but it does mean that quite large alignments are missed.

Thanks,

Theo