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Article

Strain-level transmission inference across multi-kingdom metagenomic data using TRACS.

Nature microbiology - 1 Jun 2026

Tonkin-Hill Gerry, Shao Yan, Zarebski Alexander E, Mallawaarachchi Sudaraka, Xie Ouli, Mäklin Tommi, Thorpe Harry A, Davies Mark R, Bentley Stephen D, Lawley Trevor D, Corander Jukka

Abstract excerpt

Coexisting strains of the same species within metagenomic data pose a substantial challenge to inferring transmission of pathogenic and commensal microbes. Here we present TRAnsmission Clustering of Strains (TRACS), a highly accurate algorithm for estimating genetic distances between strains at the level of individual single nucleotide polymorphisms, which is robust to intra-species diversity within the host....

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Identifiers

PMID: 42032281
DOI: 10.1038/s41564-026-02339-x
PMCID: PMC13236588

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