StainedGlass: Interactive visualization of massive tandem repeat structures with identity heatmaps

Abstract Summary Visualization and analysis of genomic repeats is typically accomplished through the use of dot plots; however, the emergence of telomere-to-telomere assemblies with multi-megabase repeats requires new visualization strategies. Here, we introduce StainedGlass which can generate publication quality figures and interactive visualizations that depict the identity and orientation of multi-megabase repeat structures at a genome-wide scale. The tool can rapidly reveal higher-order structures and improve the inference of evolutionary history for some of the most complex regions of genomes. Availability and implementation StainedGlass is implemented using Snakemake and is available open source under the MIT license at https://mrvollger.github.io/StainedGlass/ . Contact mvollger@uw.edu