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

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Traditional genomic repeat visualization methods like dot plots are insufficient for large-scale, multi-megabase repeats found in telomere-to-telomere assemblies.
• Analyzing complex genomic regions, particularly those with extensive tandem repeats, presents significant challenges for current bioinformatics tools.

Purpose of the Study:

• To introduce StainedGlass, a novel tool for visualizing and analyzing multi-megabase tandem repeat structures at a genome-wide scale.
• To provide researchers with a method for generating publication-quality figures and interactive visualizations of complex genomic repeat architectures.

Main Methods:

• Development of StainedGlass, a software tool implemented using Snakemake.
• Application of StainedGlass for genome-wide visualization of multi-megabase tandem repeat identity and orientation.

Main Results:

• StainedGlass effectively depicts multi-megabase tandem repeat structures, revealing higher-order organization.
• The tool facilitates rapid analysis and improves the inference of evolutionary history in complex genomic regions.

Conclusions:

• StainedGlass offers a powerful new strategy for visualizing and analyzing large-scale genomic repeats.
• This tool enhances the study of complex genomic structures and evolutionary processes.