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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\n                    <jats:bold>Pop<\/jats:bold>\n                    ulation analysis\n                    <jats:bold>PIPE<\/jats:bold>\n                    line (PopPIPE) which combines rapid reference-free genome analysis methods to analyse bacterial genomes across these two scales, splitting whole populations into subclusters and detecting plausible transmission events within closely related clusters. We use k-mer sketching to split populations into strains, followed by split k-mer analysis and recombination removal to create alignments and subclusters within these strains. We first show that this approach creates high-quality subclusters on a population-wide dataset of\n                    <jats:italic>Streptococcus pneumoniae<\/jats:italic>\n                    . When applied to nosocomial vancomycin-resistant\n                    <jats:italic>Enterococcus faecium<\/jats:italic>\n                    samples, PopPIPE finds transmission clusters that are more epidemiologically plausible than core genome or multilocus sequence typing (MLST) approaches. Our pipeline is rapid and reproducible, creates interactive visualizations and can easily be reconfigured and re-run on new datasets. Therefore, PopPIPE provides a user-friendly pipeline for analyses spanning species-wide clustering to outbreak investigations.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.001404","type":"journal-article","created":{"date-parts":[[2025,4,28]],"date-time":"2025-04-28T14:15:28Z","timestamp":1745849728000},"source":"Crossref","is-referenced-by-count":3,"title":["Integrated population clustering and genomic epidemiology with PopPIPE"],"prefix":"10.1099","volume":"11","author":[{"given":"Martin P.","family":"McHugh","sequence":"first","affiliation":[{"name":"Division of Infection and Global Health, University of St Andrews, St Andrews KY16 9AJ, UK"},{"name":"Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samuel T.","family":"Horsfield","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton CB10 1SD, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johanna","family":"von Wachsmann","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton CB10 1SD, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacqueline","family":"Toussaint","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton CB10 1SD, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kerry A.","family":"Pettigrew","sequence":"additional","affiliation":[{"name":"Present address: School of Health and Life Sciences, Teesside University, Middlesbrough TS1 3BX, UK"},{"name":"Division of Infection and Global Health, University of St Andrews, St Andrews KY16 9AJ, UK"},{"name":"Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elzbieta","family":"Czarniak","sequence":"additional","affiliation":[{"name":"Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas J.","family":"Evans","sequence":"additional","affiliation":[{"name":"School of Infection and Immunity, University of Glasgow, Glasgow G12 8QQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alistair","family":"Leanord","sequence":"additional","affiliation":[{"name":"Scottish Microbiology Reference Laboratories, Glasgow Royal Infirmary, Glasgow G4 0SF, UK"},{"name":"School of Infection and Immunity, University of Glasgow, Glasgow G12 8QQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luke","family":"Tysall","sequence":"additional","affiliation":[{"name":"Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen H.","family":"Gillespie","sequence":"additional","affiliation":[{"name":"Division of Infection and Global Health, University of St Andrews, St Andrews KY16 9AJ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kate E.","family":"Templeton","sequence":"additional","affiliation":[{"name":"Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew T. 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