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Article

Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions.

Molecular biology and evolution - 1 Mar 2019

Stimson James, Gardy Jennifer, Mathema Barun, Crudu Valeriu, Cohen Ted, Colijn Caroline

Abstract excerpt

Whole-genome sequencing (WGS) is increasingly used to aid the understanding of pathogen transmission. A first step in analyzing WGS data is usually to define "transmission clusters," sets of cases that are potentially linked by direct transmission. This is often done by including two cases in the same cluster if they are separated by fewer single-nucleotide polymorphisms (SNPs) than a specified threshold....

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Methodology Data sources Editorial policy Privacy About Contact Helena Bioinformatics

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PMID: 30690464
DOI: 10.1093/molbev/msy242
PMCID: PMC6389316

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