Mitchell R Vollger1, Peter Kerpedjiev2, Adam M Phillippy3, Evan E Eichler1,4. 1. Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA. 2. Reservoir Genomics LLC, Oakland, CA, 94619, USA. 3. Genome Informatics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA. 4. Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.
Abstract
SUMMARY: 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 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/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: 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 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/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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