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