Maast

Maast performs SNP genotyping of microbial strains by selecting representative conspecific genomes and applying whole-genome alignment combined with k-mer exact matching to enable scalable population genetic analyses.

Key Features:

• Representative genome selection: Heuristically identifies a minimal set of diverse conspecific genomes from available data to reduce redundancy.
• SNP panel construction: Constructs species-specific SNP panels tailored to the curated representative genomes.
• Hybrid genotyping approach: Integrates whole-genome alignment with k-mer exact matching for SNP identification.
• Scalability: Enables genotyping across thousands of microbial strains while addressing conspecific redundancy.
• High specificity and speed: Employs k-mer exact matching to provide precise and rapid SNP calls.
• Population genetic meta-analysis: Facilitates large-scale population genetic analyses across many strains.

Scientific Applications:

• Helicobacter pylori genotyping: Genotyping thousands of Helicobacter pylori strains to analyze within-species variation.
• SARS-CoV-2 diversification tracking: Tracking diversification patterns of SARS-CoV-2 to study viral evolution and spread.
• Microbial population genetics and epidemiology: Enabling studies of pathogen evolution, transmission dynamics, and identification of potential therapeutic targets.

Methodology:

Heuristically selects a minimal representative set of conspecific genomes, constructs species-specific SNP panels, and performs genotyping using whole-genome alignment combined with k-mer exact matching.