%0 Journal Article
%T ModDotPlot-rapid and interactive visualization of tandem repeats.
%A Sweeten AP
%A Schatz MC
%A Phillippy AM
%J Bioinformatics
%V 40
%N 8
%D 2024 Aug 2
%M 39110522
%F 6.931
%R 10.1093/bioinformatics/btae493
%X <B>BACKGROUND: </B>A common method for analyzing genomic repeats is to produce a sequence similarity matrix visualized via a dot plot. Innovative approaches such as StainedGlass have improved upon this classic visualization by rendering dot plots as a heatmap of sequence identity, enabling researchers to better visualize multi-megabase tandem repeat arrays within centromeres and other heterochromatic regions of the genome. However, computing the similarity estimates for heatmaps requires high computational overhead and can suffer from decreasing accuracy.<BR><B>RESULTS: </B>In this work, we introduce ModDotPlot, an interactive and alignment-free dot plot viewer. By approximating average nucleotide identity via a k-mer-based containment index, ModDotPlot produces accurate plots orders of magnitude faster than StainedGlass. We accomplish this through the use of a hierarchical modimizer scheme that can visualize the full 128 Mb genome of Arabidopsis thaliana in under 5 min on a laptop. ModDotPlot is bundled with a graphical user interface supporting real-time interactive navigation of entire chromosomes.<BR><B>METHODS: </B>ModDotPlot is available at https://github.com/marbl/ModDotPlot.