{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T03:26:28Z","timestamp":1774927588731,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2019,5,22]],"date-time":"2019-05-22T00:00:00Z","timestamp":1558483200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"International DFG Research Training Group GRK"},{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000038","name":"NSERC","doi-asserted-by":"publisher","award":["RGPIN-2017-03986"],"award-info":[{"award-number":["RGPIN-2017-03986"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Plasmids are ubiquituous in bacterial genomes, and have been shown to be involved in important evolutionary processes, in particular the acquisition of antimicrobial resistance. However separating chromosomal contigs from plasmid contigs and assembling the later is a challenging problem.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We introduce HyAsP, a tool that identifies, bins and assembles plasmid contigs following a hybrid approach based on a database of known plasmids genes and a greedy assembly algorithm. We test HyAsP on a large sample of bacterial datasets and observe that it generally outperforms other tools.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/cchauve\/HyAsP.<\/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\/btz413","type":"journal-article","created":{"date-parts":[[2019,5,14]],"date-time":"2019-05-14T11:42:11Z","timestamp":1557834131000},"page":"4436-4439","source":"Crossref","is-referenced-by-count":24,"title":["HyAsP, a greedy tool for plasmids identification"],"prefix":"10.1093","volume":"35","author":[{"given":"Robert","family":"M\u00fcller","sequence":"first","affiliation":[{"name":"Computational Methods for the Analysis of the Diversity and Dynamics of Genomes, Bielefeld University , 33615 Bielefeld, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9837-1878","authenticated-orcid":false,"given":"Cedric","family":"Chauve","sequence":"additional","affiliation":[{"name":"Department of Mathematics, Simon Fraser University , Vancouver, BC V5A 1S6, Canada"}]}],"member":"286","published-online":{"date-parts":[[2019,5,22]]},"reference":[{"key":"2023062712490295400_btz413-B1","doi-asserted-by":"crossref","first-page":"3380","DOI":"10.1093\/bioinformatics\/btw493","article-title":"plasmidSPAdes: assembling plasmids from whole genome sequencing data","volume":"32","author":"Antipov","year":"2016","journal-title":"Bioinformatics"},{"key":"2023062712490295400_btz413-B2","article-title":"On the (im)possibility of reconstructing plasmids from whole-genome short-read sequencing data","volume":"3","author":"Arredondo-Alonso","year":"2017","journal-title":"Microb. Genome"},{"key":"2023062712490295400_btz413-B3","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1016\/j.ijmm.2013.02.001","article-title":"Plasmids and the spread of resistance","volume":"303","author":"Carattoli","year":"2013","journal-title":"Int. J. Med. Microbiol"},{"key":"2023062712490295400_btz413-B4","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.plasmid.2018.09.010","article-title":"Plasmid-mediated resistance is going wild","volume":"99","author":"Dolejska","year":"2018","journal-title":"Plasmids"},{"key":"2023062712490295400_btz413-B5","article-title":"Assessing the heterogeneity of in silico plasmid predictions based on whole-genome-sequenced clinical isolates","author":"Laczny","year":"2017","journal-title":"Brief. Bioinform"},{"key":"2023062712490295400_btz413-B6","doi-asserted-by":"crossref","first-page":"182","DOI":"10.3389\/fmicb.2017.00182","article-title":"Plasmid classification in an era of whole-genome sequencing: application in studies of antibiotic resistance epidemiology","volume":"8","author":"Orlek","year":"2017","journal-title":"Front. Microbiol"},{"key":"2023062712490295400_btz413-B7","article-title":"MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies","volume":"4","author":"Robertson","year":"2018","journal-title":"Microb. Genome"},{"key":"2023062712490295400_btz413-B8","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1093\/bioinformatics\/btw651","article-title":"Recycler: an algorithm for detecting plasmids from de novo assembly graphs","volume":"33","author":"Rozov","year":"2017","journal-title":"Bioinformatics"},{"key":"2023062712490295400_btz413-B9","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pcbi.1005595","article-title":"Unicycler: resolving bacterial genome assemblies from short and long sequencing reads","volume":"13","author":"Wick","year":"2017","journal-title":"PLoS Comput. Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz413\/28789107\/btz413.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/21\/4436\/50721720\/bioinformatics_35_21_4436.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/21\/4436\/50721720\/bioinformatics_35_21_4436.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,27]],"date-time":"2023-06-27T12:49:19Z","timestamp":1687870159000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/21\/4436\/5497247"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,5,22]]},"references-count":9,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2019,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz413","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,11,1]]},"published":{"date-parts":[[2019,5,22]]}}}