GraphSNP

GraphSNP visualizes pairwise single-nucleotide polymorphism (SNP) distance networks to represent genetic relationships for genomic epidemiology and transmission analysis.

Key Features:

• Pairwise SNP distance calculation: Computes pairwise SNP distances between genomes to quantify genetic divergence.
• Network construction: Constructs SNP distance networks that represent genetic relationships among isolates.
• Interactive visualization: Provides interactive visual exploration of pairwise SNP distance networks and their topology.
• Rapid network generation: Enables rapid construction of SNP distance networks for timely analyses such as outbreak investigations.
• SNP distance distribution analysis: Summarizes and visualizes the distribution of pairwise SNP distances to assess genetic diversity.
• Cluster identification: Identifies clusters of related isolates within SNP distance networks.
• Transmission route reconstruction: Supports reconstruction of potential transmission routes from SNP distance networks.

Scientific Applications:

• Outbreak investigation: Facilitates identification of infection sources and transmission patterns during outbreaks.
• Transmission network analysis: Maps putative transmission links and spread of pathogens using SNP distance networks.
• Cluster analysis: Assesses genetic relatedness and grouping of isolates to detect epidemiologically relevant clusters.
• Multi-drug resistant bacterial outbreak analysis: Applies SNP distance network analysis to multi-drug resistant bacterial outbreaks in healthcare settings.

Methodology:

Calculates pairwise SNP distances and constructs networks from those distances to represent genetic relationships among isolates.