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README.md

dotPlotly example

Compare diploid Brassica rapa and allo-tetraploid Brassica napus (hybrid of B. rapa and B. oleracea)

NB: Some differences between below dot plots (e.g. sparseness of alignments) may be due to filtering parameter settings (-m and -q).

1. Mummer example

nucmer --maxmatch -l 80 -c 100 Brassica_rapa.faa Brassica_napus_rape.faa -p Brapa_Bnapus.nucmer
delta-filter -r Brapa_Bnapus.nucmer.delta > Brapa_Bnapus.nucmer.delta.filter
show-coords -c Brapa_Bnapus.nucmer.delta.filter > Brapa_Bnapus.nucmer.delta.filter.coords

Make dot plot:

../mummerCoordsDotPlotly.R -i Brapa_Bnapus.nucmer.delta.filter.coords -o Brapa_Bnapus.nucmer.plot -m 1000 -q 300000 -k 10 -s -t -l -p 12

Dotplot

2. Minimap2 example

(16 seconds on a Macbook Pro)

minimap2 -x asm5 Brassica_rapa.faa Brassica_napus_rape.faa > Brapa_Bnapus.minimap2.paf

Make dot plot:

../pafCoordsDotPlotly.R -i Brapa_Bnapus.minimap2.paf -o Brapa_Bnapus.minimap2.plot -m 2000 -q 500000 -k 10 -s -t -l -p 12

Dotplot