StainedGlass

StainedGlass visualizes sequence identity and orientation of multi-megabase genomic repeat structures to reveal higher-order organization in telomere-to-telomere assemblies and across genomes.

Key Features:

• High-quality visualization: Generates publication-quality figures that depict sequence identity and orientation of multi-megabase repeat structures across entire genomes.
• Rapid analysis: Enables rapid analysis of large genomic regions to reveal higher-order repeat structures.
• Evolutionary insights: Provides detailed visualizations of repeat architecture to support inference of evolutionary history of complex genomic regions.

Scientific Applications:

• Telomere-to-telomere assembly analysis: Characterization of multi-megabase repeats within telomere-to-telomere assemblies.
• Genome-wide repeat characterization: Application to large-scale genomic projects and studies in genomics and evolutionary biology that require visualization of complex repeat regions.

Methodology:

Implemented as a Snakemake workflow to facilitate reproducible and scalable data analyses.