THRESHER: A tool for evidence-based, phylogeny-corrected SNP thresholds for whole genome molecular epidemiology

Whole-genome sequencing (WGS) is the gold standard for bacterial pathogen surveillance, where transmission is commonly inferred by calculating pairwise single nucleotide polymorphisms (SNPs) and applying a fixed threshold below which two genomes are considered the ''same'' strain. Such cutoffs are largely arbitrary. The relationship between genetic distance and epidemiological linkage varies with sample size, sampling duration, setting, and patterns of infection and carriage. A threshold calibrated in one study may not transfer to another. To address this, we present THRESHER, a pipeline that

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