CanSNPer

CanSNPer classifies pathogen genotypes by identifying canonical single nucleotide polymorphisms (SNPs) in core genomes from whole-genome sequencing data to support molecular epidemiology and outbreak tracing.

Key Features:

• Efficient genotype classification: Uses a predefined database of canonical SNPs to determine genotypes rapidly and reproducibly from core-genome data.
• Expandable SNP database: Supports incorporation of new canonical SNPs to update classification schemes as novel variants are discovered.
• High-throughput SNP detection: Processes whole-genome sequencing data to enable high-throughput detection of canonical SNP markers across pathogen genomes.

Scientific Applications:

• Molecular epidemiology: Infers genetic relationships among pathogen strains for surveillance and epidemiological investigations.
• Outbreak investigation and source tracing: Enables tracing infection sources and monitoring disease outbreaks using genotype assignments.
• Evolutionary dynamics and phylogenetics: Supports study of pathogen evolutionary dynamics using evolutionarily stable SNP markers.

Methodology:

Processes sequence data from pathogen core genomes to identify predefined canonical SNPs selected for stability and relevance, and assigns genotypes based on those SNP markers.