covSampler

covSampler performs balanced subsampling of SARS-CoV-2 genome sequences to generate spatiotemporally and genetically representative subsets for downstream phylogenetic and evolutionary analyses.

Key Features:

• Balanced Subsampling: Incorporates both spatiotemporal distribution and genetic variation of SARS-CoV-2 genomes to produce representative subsamples that mitigate sampling bias.
• Divergent Pathways Clustering: Clusters genome sequences into "divergent pathways" defined by spatiotemporal and genetic characteristics to preserve evolutionary diversity.
• Subsampling Strategies: Provides two explicit strategies—representative subsampling and comprehensive subsampling—with adjustable parameters to tailor dataset reduction.
• Efficiency and Stability: Performance tests validate the tool's efficiency and stability when processing large genomic datasets.

Scientific Applications:

• Phylogenetic analysis: Generates representative subsets for more accurate phylogenetic inference of SARS-CoV-2 evolutionary relationships.
• Transmission dynamics: Produces balanced samples that support analyses of geographic and temporal patterns of viral spread.
• Mutation pathway analysis: Preserves genetic diversity to inform investigation of potential mutation pathways and evolutionary trajectories.

Methodology:

CovSampler clusters sequences into "divergent pathways" defined by spatiotemporal and genetic characteristics, then performs subsampling that balances spatiotemporal distribution and genetic diversity using either representative or comprehensive strategies with adjustable parameters.