Sequence tube maps

Sequence tube maps renders graph genomes as tube-map–style visualizations to make vg-produced sequence graphs interpretable for analyses such as polymorphism representation and sequencing-read mapping.

Key Features:

• Graph Genome Visualization: Transforms graph genomes generated by vg into tube-map–style visualizations that represent nodes and paths of genome graphs.
• Efficient Data Representation: Uses graph genomes as compact data structures to encode multiple genomic sequences, polymorphisms, and information for mapping sequencing reads with greater sensitivity than a single haploid reference.
• Tube-map Layout Methods: Adapts established public transport tube map design methods to simplify and clarify the topology of genome graphs for interpretation.
• JavaScript Implementation: Provided as a JavaScript module for rendering graph genome visualizations.

Scientific Applications:

• Genomic Research: Aids interpretation and analysis of complex graph-based genomic data structures.
• Polymorphism Analysis: Enables inspection and visualization of polymorphisms encoded within graph genomes.
• Sequencing Read Mapping: Supports interpretation and validation of variation-aware sequencing read mappings with increased sensitivity relative to haploid references.

Methodology:

Implements a JavaScript module to render graph genomes produced by vg, employing well-studied computer science techniques and methods adapted from public transport tube map design to layout and visualize genome graphs.