Integrated population clustering and genomic epidemiology with PopPIPE.

ABSTRACT: Genetic distances between bacterial DNA sequences can be used to cluster populations into closely related subpopulations and as an additional source of information when detecting possible transmission events. Due to their variable gene content and order, reference-free methods offer more sensitive detection of genetic differences, especially among closely related samples found in outbreaks. However, across longer genetic distances, frequent recombination can make calculation and interpretation of these differences more challenging, requiring significant bioinformatic expertise and manual intervention during the analysis process. Here, we present a Population analysis PIPEline (PopPIPE) which combines rapid reference-free genome analysis methods to analyse bacterial genomes ac

SUBMITTER: McHugh MP 

PROVIDER: S-EPMC12038005 | biostudies-literature | 2025 Apr

REPOSITORIES: biostudies-literature