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

The visualization and analysis of genomic repeats is typically accomplished using 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 tandem 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 available open source under the MIT license at https://mrvollger.github.io/StainedGlass/. Contact: mvollger@uw.edu or eee@gs.washington.edu Supplementary information: Supplementary data are available at Bioinformatics online.