{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,12]],"date-time":"2025-11-12T13:57:44Z","timestamp":1762955864155,"version":"3.37.3"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2018,3,28]],"date-time":"2018-03-28T00:00:00Z","timestamp":1522195200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100020064","name":"New Zealand Food Safety Science & Research Centre","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100020064","id-type":"DOI","asserted-by":"crossref"}]}],"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>Motivation<\/jats:title>\n                  <jats:p>Large-scale whole-genome sequencing dataset-based studies are becoming increasingly common in pathogen surveillance and outbreak investigations. A highly discriminative and time-efficient bioinformatics tool is needed to transform large amounts of sequencing data into usable biological information. To replace the intuitive, yet inefficient, way of gene-by-gene allele calling algorithm, a new algorithm using genome-by-genome approach was developed.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Tests showed that the program equipped with the new algorithm achieved significant improvements in allele calling efficiency compared to a conventional gene-by-gene approach. The new program, Fast-GeP, rendered a fast and easy way to infer high-resolution genealogical relationships between bacterial isolates using whole-genome sequencing data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>FAST-GeP is freely available from: https:\/\/github.com\/jizhang-nz\/fast-GeP.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty195","type":"journal-article","created":{"date-parts":[[2018,3,28]],"date-time":"2018-03-28T03:12:03Z","timestamp":1522206723000},"page":"3025-3027","source":"Crossref","is-referenced-by-count":29,"title":["Genome-by-genome approach for fast bacterial genealogical relationship evaluation"],"prefix":"10.1093","volume":"34","author":[{"given":"Ji","family":"Zhang","sequence":"first","affiliation":[{"name":"mEpiLab, New Zealand Food Safety Science & Research Centre, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand"}]},{"given":"Yanwen","family":"Xiong","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China"}]},{"given":"Lynn","family":"Rogers","sequence":"additional","affiliation":[{"name":"mEpiLab, New Zealand Food Safety Science & Research Centre, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand"}]},{"given":"Glen P","family":"Carter","sequence":"additional","affiliation":[{"name":"Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne, Melbourne, Australia"}]},{"given":"Nigel","family":"French","sequence":"additional","affiliation":[{"name":"mEpiLab, New Zealand Food Safety Science & Research Centre, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand"}]}],"member":"286","published-online":{"date-parts":[[2018,3,28]]},"reference":[{"key":"2023061313384213300_bty195-B1","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat. Methods"},{"key":"2023061313384213300_bty195-B2","doi-asserted-by":"crossref","first-page":"421.","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023061313384213300_bty195-B3","doi-asserted-by":"crossref","first-page":"2526","DOI":"10.1128\/JCM.00066-13","article-title":"Real-time genomic epidemiological evaluation of human Campylobacter isolates by use of whole-genome multilocus sequence typing","volume":"51","author":"Cody","year":"2013","journal-title":"J. Clin. Microbiol"},{"key":"2023061313384213300_bty195-B4","doi-asserted-by":"crossref","first-page":"1005","DOI":"10.1099\/mic.0.055459-0","article-title":"Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain","volume":"158","author":"Jolley","year":"2012","journal-title":"Microbiol."},{"key":"2023061313384213300_bty195-B5","doi-asserted-by":"crossref","first-page":"595.","DOI":"10.1186\/1471-2105-11-595","article-title":"BIGSdb: scalable analysis of bacterial genome variation at the population level","volume":"11","author":"Jolley","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023061313384213300_bty195-B6","doi-asserted-by":"crossref","first-page":"1269","DOI":"10.1128\/JCM.00017-17","article-title":"Whole-genome sequencing in epidemiology of Campylobacter jejuni infections","volume":"55","author":"Llarena","year":"2017","journal-title":"J. Clin. Microbiol"},{"key":"2023061313384213300_bty195-B7","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1146\/annurev.micro.59.030804.121325","article-title":"Multilocus sequence typing of bacteria","volume":"60","author":"Maiden","year":"2006","journal-title":"Annu. Rev. Microbiol"},{"key":"2023061313384213300_bty195-B8","doi-asserted-by":"crossref","first-page":"728","DOI":"10.1038\/nrmicro3093","article-title":"MLST revisited: the gene-by-gene approach to bacterial genomics","volume":"11","author":"Maiden","year":"2013","journal-title":"Nat. Rev. Microbiol"},{"key":"2023061313384213300_bty195-B9","doi-asserted-by":"crossref","first-page":"261","DOI":"10.3390\/genes3020261","article-title":"A gene-by-gene approach to bacterial population genomics: whole genome MLST of Campylobacter","volume":"3","author":"Sheppard","year":"2012","journal-title":"Genes"},{"key":"2023061313384213300_bty195-B151","doi-asserted-by":"crossref","first-page":"909","DOI":"10.3389\/fmicb.2017.00909","article-title":"Food safety in the age of next generation sequencing, bioinformatics, and open data access","volume":"8","author":"Taboada","year":"2017","journal-title":"Front Microbiol."},{"key":"2023061313384213300_bty195-B10","doi-asserted-by":"crossref","first-page":"1765","DOI":"10.1128\/JCM.00051-15","article-title":"Refinement of whole-genome multilocus sequence typing analysis by addressing gene paralogy","volume":"53","author":"Zhang","year":"2015","journal-title":"J. Clin. Microbiol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/17\/3025\/50581988\/bioinformatics_34_17_3025.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/17\/3025\/50581988\/bioinformatics_34_17_3025.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,13]],"date-time":"2023-06-13T13:40:02Z","timestamp":1686663602000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/17\/3025\/4956016"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,3,28]]},"references-count":11,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2018,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty195","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2018,9,1]]},"published":{"date-parts":[[2018,3,28]]}}}