D-GENIES for Dotplot large Genomes in an Interactive, Efficient and Simple way is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualisation.
We use minimap version 2 to align the two genomes. Then, the PAF file is parsed and plotted into an interactive plot written with d3.js library.
D-Genies is available under the GNU General Public License (GPL). The package is coming with full documentation and test data. Sources are available here.