MUMmer on large genomes memo

nucmer -l 1000 -g 1000 --maxmatch --nosimplify --prefix=test1 GenomeX.fa GenomeY.fa

nucmer -l 1000 -g 1000 --prefix=test2 GenomeX.fa GenomeY.fa

 

nucmer -l  300 -g 1000 --prefix=test2 GenomeX.fa GenomeY.fa

-l Minimum length of an maximal exact match (default 20)
-g Maximum gap between two adjacent matches in a cluster (default 90)
--maxmatch Use all anchor matches regardless of their uniqueness
--[no]simplify Simplify alignments by removing shadowed clusters. Turn this option off if aligning a sequence to itself to look for repeats (default --simplify)

Although MUMmer was not specifically designed to identify repeats, it does has a few methods of identifying exact and exact tandem repeats. In addition to these methods, the nucmer alignment script can be used to align a sequence (or set of sequences) to itself. By ignoring all of the hits that have the same coordinates in both inputs, one can generate a list of inexact repeats. When using this method of repeat detection, be sure to set the --maxmatch and --nosimplify options to ensure the correct results.

mummerplot test2.delta -t png -p test2.plot.D (first try with default layout)

mummerplot -l test2.delta -t png -p test2.plot.L (second try with all hits on main diagonal)

mummerplot "test2.delta" --filter --png --large --prefix "test2-Plot" --title "test2"

To get SVG plot you have to edit out.gp file, find and change following lines:

set terminal svg size 1600,1600 font "Helvetica-Bold,24 bold"

set terminal svg size 1200,1200 font "Helvetica-Bold,16 bold"

 

set output "test2.X.svg"

.....

set style line 1  lt 1 lw 3 pt 6 ps 0.5

set style line 2  lt 3 lw 3 pt 6 ps 0.5

set style line 3  lt 2 lw 3 pt 6 ps 0.5

set grid layerdefault linewidth 6

set style line 1  lt 1 lw 3 pt 6 ps 0.3
set style line 2  lt 3 lw 3 pt 6 ps 0.3
set style line 3  lt 2 lw 3 pt 6 ps 0.3
set grid layerdefault linewidth 3

and then re-run gnuplot

http://mummer.sourceforge.net/manual/