genome-sampler

genome-sampler performs reproducible subsampling of SARS-CoV-2 genomes to support genomic epidemiology, phylogenetic inference, and variant analyses.

Key Features:

• Modular Design: Modular architecture enables independent or combined application of multiple sampling strategies and benchmarking of sampling approaches.
• Sampling Axes: Enables sampling by time of isolation, location of isolation, and viral diversity to capture temporal, geographic, and genetic variation.
• Sampling Strategies: Supports multiple sampling methods, including random sampling and diversity-focused subsampling.
• Reproducibility and Provenance Tracking: Implements a QIIME 2 plugin interface to provide retrospective data provenance tracking for reproducible analyses.

Scientific Applications:

• Phylogenetic Analyses: Reduces dataset size while maintaining representativeness to enable computationally feasible phylogenetic inference of SARS-CoV-2.
• Epidemiological Studies: Supports analysis of spatiotemporal spread and transmission dynamics using subsampled genomes.
• Variant Analysis: Facilitates identification and characterization of emerging SARS-CoV-2 variants from large repositories such as GISAID.

Methodology:

Performs systematic subsampling of viral genomes with a modular framework that integrates multiple sampling methods (including random sampling) and records processing steps via QIIME 2 retrospective provenance tracking.