VaST

VaST identifies and selects the minimal set of informative genomic variant sites for targeted PCR amplicon sequencing (TAS) to enable strain-level differentiation within bacterial species for applications such as biodefense, forensics, clinical diagnostics, and outbreak investigation.

Key Features:

• Optimization of Target Sites: Identifies the minimum number of genomic variant sites required to maximize strain-level resolution, achieving reductions in target number ranging from 20% to 88% compared to traditional approaches.
• Strain-Level Resolution: Generates unique haplotypes for each strain to provide high-resolution discrimination within strain complexes for TAS assays.
• Conserved Primer Regions: Selects targets that contain conserved primer regions to enable amplification across all known strains within the complex.
• Inclusion of Basal Variants: Favors targets containing basal variants to enhance robustness of identification, including for previously unseen strains.
• Efficient Design Process: Achieves significant strain resolution rapidly, typically within the first 20 selected targets.

Scientific Applications:

• TAS panel design and validation: Facilitates design and computational/experimental validation of TAS-based panels for pathogenic bacterial species, enabling accurate placement of strains phylogenetically, including strains not present in the original panel.
• Public health and security applications: Supports biodefense, forensic, clinical diagnostics, and outbreak investigation efforts by providing high-resolution strain typing information.

Methodology:

Analyzes a provided set of variant sites and employs an algorithm to determine the optimal combination of targets that maximizes strain resolution, with options to adjust run-time parameters.