{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,27]],"date-time":"2026-05-27T15:48:50Z","timestamp":1779896930792,"version":"3.53.1"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2020,4,9]],"date-time":"2020-04-09T00:00:00Z","timestamp":1586390400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Joint Programming Initiative in Antimicrobial Resistance"},{"DOI":"10.13039\/100013281","name":"JPIAMR","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100013281","id-type":"DOI","asserted-by":"publisher"}]},{"name":"STARCS","award":["JPIAMR2016-AC16\/00039"],"award-info":[{"award-number":["JPIAMR2016-AC16\/00039"]}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["742158"],"award-info":[{"award-number":["742158"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Plasmids can horizontally transmit genetic traits, enabling rapid bacterial adaptation to new environments and hosts. Short-read whole-genome sequencing data are often applied to large-scale bacterial comparative genomics projects but the reconstruction of plasmids from these data is facing severe limitations, such as the inability to distinguish plasmids from each other in a bacterial genome. We developed gplas, a new approach to reliably separate plasmid contigs into discrete components using sequence composition, coverage, assembly graph information and network partitioning based on a pruned network of plasmid unitigs. Gplas facilitates the analysis of large numbers of bacterial isolates and allows a detailed analysis of plasmid epidemiology based solely on short-read sequence data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Gplas is written in R, Bash and uses a Snakemake pipeline as a workflow management system. Gplas is available under the GNU General Public License v3.0 at https:\/\/gitlab.com\/sirarredondo\/gplas.git.<\/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\/btaa233","type":"journal-article","created":{"date-parts":[[2020,4,2]],"date-time":"2020-04-02T07:16:34Z","timestamp":1585811794000},"page":"3874-3876","source":"Crossref","is-referenced-by-count":36,"title":["gplas: a comprehensive tool for plasmid analysis using short-read graphs"],"prefix":"10.1093","volume":"36","author":[{"given":"Sergio","family":"Arredondo-Alonso","sequence":"first","affiliation":[{"name":"Department of Medical Microbiology , University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Bootsma","sequence":"additional","affiliation":[{"name":"Department of Epidemiology , Julius Center for Health Sciences and Primary Care of the UMC Utrecht"},{"name":"Department of Mathematics , Faculty of Sciences, Utrecht University, 3584 CX Utrecht, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ya\u00efr","family":"Hein","sequence":"additional","affiliation":[{"name":"Department of Mathematics , Faculty of Sciences, Utrecht University, 3584 CX Utrecht, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Malbert R C","family":"Rogers","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology , University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jukka","family":"Corander","sequence":"additional","affiliation":[{"name":"Department of Parasites and Microbes , Wellcome Sanger Institute, Hinxton, Saffron Walden CB10 1RQ, UK"},{"name":"Department of Biostatistics , University of Oslo, 0317 Oslo, Norway"},{"name":"Department of Mathematics and Statistics , Helsinki Institute of Information Technology (HIIT), University of Helsinki, FI-00014 Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rob J L","family":"Willems","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology , University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anita C","family":"Sch\u00fcrch","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology , University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,4,9]]},"reference":[{"key":"2023063011293372200_btaa233-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":"2023063011293372200_btaa233-B2","article-title":"mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species","volume":"4, e000224","author":"Arredondo-Alonso","year":"2018","journal-title":"Microb. 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