SVAMP

SVAMP provides visualization and analysis of genomic variants (SNPs and indels) from VCF files integrated with geographical metadata for epidemiological and population-genetic investigations.

Key Features:

• Real-time visualization: Visualizes allele frequency maps, geographical distributions of isolates, and density metrics including SNP density, GC content, and variation density.
• Phylogenetic analysis: Generates phylogenetic trees to infer evolutionary relationships among samples.
• Principal Coordinate Analysis (PCoA): Performs PCoA for multidimensional scaling to explore genetic diversity and population structure.
• Tajima's D metric: Calculates and visualizes Tajima's D to detect departures from neutrality and infer selection pressures.
• VCF and metadata processing: Processes variant call format (VCF) files together with associated metadata for integrated analyses.
• Scalability and accuracy: Demonstrated by tracking a methicillin-resistant Staphylococcus aureus outbreak across 15 countries and analyzing 245 Plasmodium falciparum isolates from three continents.

Scientific Applications:

• Epidemiological surveillance: Integrates genomic variants with geographic data to track outbreaks and transmission across regions.
• Population genetics: Assesses genetic diversity, population structure, and selection using PCoA and Tajima's D.
• Pathogen spread mapping: Maps allele frequencies and isolate distributions to study geographic spread of pathogens.
• Evolutionary inference: Uses phylogenetic trees to infer evolutionary relationships among isolates.

Methodology:

Processes VCF files and associated metadata, generates phylogenetic trees, performs principal coordinate analysis (PCoA), computes Tajima's D, and produces allele frequency maps and density metrics (SNP, GC content, variation density).