cSupB

cSupB implements a tri-tuple coordinate system to organize genome-graph pangenomes for representation of species- or population-specific haplotype sequences and to enable detection of small insertions and deletions (<50 bp) using complete topological information.

Key Features:

• Tri-Tuple Coordinate System: Integrates an offset value, topological structure, and sample information to align genome-graph data with linear-reference–style coordinates.
• Superbubble Organization: Organizes haplotype sequences into superbubbles to reduce structural complexity and simplify interpretation of genome graph regions.
• Variant Detection: Uses complete topological information to detect small insertions and deletions (<50 bp) in highly similar samples, validated on simulated datasets.
• Adaptability to Complex Structures: Relaxes directed acyclic graph (DAG) constraints to accommodate complex cycle structures and to operate on colored directed acyclic graphs.
• Facilitation of Genomic Diversity Analysis: Structures genome-graph data to support analysis of individual haplotype variants and population genomic diversity.

Scientific Applications:

• Pangenomics: Provides a structured coordinate and superbubble framework for representation and analysis of pangenomes and haplotype-resolved assemblies.
• Variant Analysis: Enables high-resolution detection of small indels in closely related samples or population cohorts.
• Genomic Diversity Studies: Supports investigation of haplotype variation and population-level genetic diversity using genome graphs.

Methodology:

Combines a tri-tuple coordinate system (offset, topology, sample) with a superbubble model to partition genome graphs, leverages complete topological information to detect indels (<50 bp), and relaxes DAG constraints to handle complex cycles and colored directed acyclic graphs; variant detection was validated on simulated datasets.