{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,19]],"date-time":"2026-03-19T05:17:35Z","timestamp":1773897455083,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"17","funder":[{"name":"National Institute for Health Research Health Protection Research Unit in GI Infections"},{"name":"NHS"},{"DOI":"10.13039\/100006662","name":"NIHR","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006662","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000276","name":"Department of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000276","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002141","name":"Public Health England","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002141","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Real-time surveillance of infectious disease using whole genome sequencing data poses challenges in both result generation and communication. SnapperDB represents a set of tools to store bacterial variant data and facilitate reproducible and scalable analysis of bacterial populations. We also introduce the \u2018SNP address\u2019 nomenclature to describe the relationship between isolates in a population to the single nucleotide resolution. We announce the release of SnapperDB v1.0 a program for scalable routine SNP analysis and storage of microbial populations.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>SnapperDB is implemented as a python application under the open source BSD license. All code and user guides are available at https:\/\/github.com\/phe-bioinformatics\/snapperdb. Reference genomes and SnapperDB configs are available at https:\/\/github.com\/phe-bioinformatics\/snapperdb_references.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty212","type":"journal-article","created":{"date-parts":[[2018,4,4]],"date-time":"2018-04-04T15:12:36Z","timestamp":1522854756000},"page":"3028-3029","source":"Crossref","is-referenced-by-count":195,"title":["SnapperDB: a database solution for routine sequencing analysis of bacterial isolates"],"prefix":"10.1093","volume":"34","author":[{"given":"Timothy","family":"Dallman","sequence":"first","affiliation":[{"name":"Gastrointestinal Bacteria Reference Unit, National Infections Service, Public Health England, London, UK"}]},{"given":"Philip","family":"Ashton","sequence":"additional","affiliation":[{"name":"Gastrointestinal Bacteria Reference Unit, National Infections Service, Public Health England, London, UK"},{"name":"Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam"}]},{"given":"Ulf","family":"Schafer","sequence":"additional","affiliation":[{"name":"Infectious Disease Informatics, National Infections Service, Public Health England, London, UK"}]},{"given":"Aleksey","family":"Jironkin","sequence":"additional","affiliation":[{"name":"Infectious Disease Informatics, National Infections Service, Public Health England, London, UK"}]},{"given":"Anais","family":"Painset","sequence":"additional","affiliation":[{"name":"Gastrointestinal Bacteria Reference Unit, National Infections Service, Public Health England, London, UK"}]},{"given":"Sharif","family":"Shaaban","sequence":"additional","affiliation":[{"name":"Roslin Institute, University of Edinburgh, Scotland, UK"}]},{"given":"Hassan","family":"Hartman","sequence":"additional","affiliation":[{"name":"Gastrointestinal Bacteria Reference Unit, National Infections Service, Public Health England, London, UK"}]},{"given":"Richard","family":"Myers","sequence":"additional","affiliation":[{"name":"Infectious Disease Informatics, National Infections Service, Public Health England, London, UK"}]},{"given":"Anthony","family":"Underwood","sequence":"additional","affiliation":[{"name":"Infectious Disease Informatics, National Infections Service, Public Health England, London, UK"}]},{"given":"Claire","family":"Jenkins","sequence":"additional","affiliation":[{"name":"Gastrointestinal Bacteria Reference Unit, National Infections Service, Public Health England, London, UK"}]},{"given":"Kathie","family":"Grant","sequence":"additional","affiliation":[{"name":"Gastrointestinal Bacteria Reference Unit, National Infections Service, Public Health England, London, UK"}]}],"member":"286","published-online":{"date-parts":[[2018,4,5]]},"reference":[{"key":"2023061313390177200_bty212-B1","author":"Ashton","year":"2015"},{"key":"2023061313390177200_bty212-B2","first-page":"1","article-title":"Whole genome sequencing improved case ascertainment in an outbreak of Shiga toxin-producing Escherichia coli O157 associated with raw drinking milk","author":"Butcher","year":"2016","journal-title":"Epidemiol. 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