PANPASCO

PANPASCO performs pan-genome mapping and base-by-base pairwise single nucleotide polymorphism (SNP) distance calculations from next-generation sequencing (NGS) data to detect and analyze transmission clusters of Mycobacterium tuberculosis.

Key Features:

• Pan-Genome Mapping: Maps genomes using a pan-genome approach to capture core and accessory genes of Mycobacterium tuberculosis.
• Pairwise SNP-Distance Calculation: Computes base-by-base pairwise SNP distances, including in lineage-specific regions, to differentiate closely related strains.
• Sensitivity and Specificity: Demonstrates improved sensitivity and specificity compared to previously published methods across multiple datasets and M. tuberculosis lineages.
• Scalability for Diverse Samples: Processes large, diverse whole-genome sequencing (WGS) sample sets for population-scale transmission analyses.

Scientific Applications:

• Transmission Cluster Detection: Identifying clusters of related M. tuberculosis cases using precise genetic distance measurements.
• Outbreak Investigation: Resolving transmission links in outbreak investigations by distinguishing closely related strains.
• Lineage-Specific Analysis: Analyzing lineage-specific genomic regions to inform studies of evolution, vaccine development, and treatment strategies.

Methodology:

PANPASCO integrates pan-genome mapping with base-by-base pairwise SNP-distance calculations on next-generation sequencing (NGS) whole-genome data to capture conserved and variable (core and accessory) genomic elements across M. tuberculosis sample sets.