DTOURS: Dense-region tagging for outbreak detection using ratio statistics.

ABSTRACT: Surveillance for food safety in the United States of America is a collaborative effort among public health agencies with additional partners worldwide contributing sequence data. Assemblies in GenBank and sequence reads in the Sequence Read Archive for surveilled species are received, rapidly analyzed, and results published publicly by an automated pathogen detection pipeline at the National Center for Biotechnology Information. The pipeline detects close isolates with a recent common ancestor by finding single nucleotide polymorphisms (SNPs) in genomes for pairs of isolates. Very few vertically transmitted SNPs are expected between a pair of close isolates; any genomic region with many SNPs compared to the number of SNPs in the rest of the genome is indicative of a horizontally transferre

SUBMITTER: Wagner L 

PROVIDER: S-EPMC12074585 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature