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Nevertheless, identifying prophages within bacterial genomes remains challenging due to their heterogeneity and similarity to other mobile genetic elements. Here we present PHORAGER (Prophage Hunting, vOtu Retrieval, Annotation and Genomic ExploRation), a scalable Nextflow pipeline for the standardised identification and quality assessment of prophages from bacterial genomes. PHORAGER incorporates bacterial genome pre-processing, consolidation of predictions from multiple mining tools, annotation-based filtering to reduce false positives, and generation of ready-to-analyse summary tables. We validated PHORAGER using 30,824 publicly available ESKAPE pathogen genomes. PHORAGER recovered more high-quality prophages than individual mining tools alone, and through extensive quality assessments removed a substantial number of false-positive predictions. In total 23,132 putative prophages were identified, the majority belonging to the class\n                  <jats:italic>Caudoviricetes<\/jats:italic>\n                  , and exhibiting a high degree of host-specificity. Putative antimicrobial resistance genes were detected in 0.48% of prophages, whereas virulence factors were most abundant in\n                  <jats:italic>S. aureus<\/jats:italic>\n                  prophages. ESKAPE prophages also frequently encoded anti-phage defence systems. PHORAGER is freely available as open-source software and the ESKAPE prophage collection generated in this study provides a reusable resource for further investigations.\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>GRAPHICAL ABTRACT<\/jats:title>\n                  <jats:fig id=\"ufig1\" position=\"float\" fig-type=\"figure\" orientation=\"portrait\">\n                    <jats:graphic xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"742953v1_ufig1\" position=\"float\" orientation=\"portrait\"\/>\n                  <\/jats:fig>\n                <\/jats:sec>","DOI":"10.64898\/2026.08.05.742953","type":"posted-content","created":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T04:50:28Z","timestamp":1785991828000},"source":"Crossref","is-referenced-by-count":0,"title":["Defining the ESKAPE pathogen prophage repertoire with PHORAGER"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-8070-698X","authenticated-orcid":false,"given":"Xena","family":"Dyball","sequence":"first","affiliation":[{"name":"Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK"},{"name":"Centre for Microbial Interactions, Norwich Research Park, Norwich, NR4 7UG, UK"},{"name":"University of East Anglia, Norwich, NR4 7UG, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4125-7561","authenticated-orcid":false,"given":"Alise J","family":"Ponsero","sequence":"additional","affiliation":[{"name":"Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK"},{"name":"Centre for Microbial Interactions, Norwich Research Park, Norwich, NR4 7UG, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-8509-3069","authenticated-orcid":false,"given":"James A D","family":"Docherty","sequence":"additional","affiliation":[{"name":"Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK"},{"name":"Centre for Microbial Interactions, Norwich Research Park, Norwich, NR4 7UG, UK"},{"name":"University of East Anglia, Norwich, NR4 7UG, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7619-281X","authenticated-orcid":false,"given":"Andrea","family":"Telatin","sequence":"additional","affiliation":[{"name":"Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK"},{"name":"Centre for Microbial Interactions, Norwich Research Park, Norwich, NR4 7UG, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-7884-8532","authenticated-orcid":false,"given":"Emmanuelle H","family":"Crost","sequence":"additional","affiliation":[{"name":"Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK"},{"name":"Centre for Microbial Interactions, Norwich Research Park, Norwich, NR4 7UG, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8515-1315","authenticated-orcid":false,"given":"Nathalie","family":"Juge","sequence":"additional","affiliation":[{"name":"Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK"},{"name":"Centre for Microbial Interactions, Norwich Research Park, Norwich, NR4 7UG, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4203-2193","authenticated-orcid":false,"given":"Ryan","family":"Cook","sequence":"additional","affiliation":[{"name":"Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK"},{"name":"Centre for Microbial Interactions, Norwich Research Park, Norwich, NR4 7UG, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4826-5406","authenticated-orcid":false,"given":"Evelien M","family":"Adriaenssens","sequence":"additional","affiliation":[{"name":"Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK"},{"name":"Centre for Microbial Interactions, Norwich Research Park, Norwich, NR4 7UG, UK"},{"name":"University of East Anglia, Norwich, NR4 7UG, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026080704452205000_2026.08.05.742953v1.1","first-page":"e00052","article-title":"Are There 1031 Virus Particles on Earth, or More, or Fewer?","volume":"202","year":"2020","journal-title":"J. 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