{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T10:47:42Z","timestamp":1784630862026,"version":"3.55.0"},"reference-count":65,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T00:00:00Z","timestamp":1762819200000},"content-version":"vor","delay-in-days":10,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000016","name":"Department of Health and Human Services","doi-asserted-by":"publisher","award":["U19AI110818"],"award-info":[{"award-number":["U19AI110818"]}],"id":[{"id":"10.13039\/100000016","id-type":"DOI","asserted-by":"publisher"}]},{"name":"University of California Irvine and the Broad Institute","award":["U19AI172725"],"award-info":[{"award-number":["U19AI172725"]}]},{"name":"NIGMS of the National Institutes of Health","award":["R35GM133700"],"award-info":[{"award-number":["R35GM133700"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The ability to detect and reconstruct plasmids from genome assemblies is crucial for studying the evolution and spread of antimicrobial resistance and virulence in bacteria. Though long-read sequencing technologies have made reconstructing plasmids easier, most (97%) of the bacterial genome assemblies in the public domain are generated from short-read data. Work to compare plasmid reconstruction tools has focused primarily on Escherichia coli, leaving gaps in our understanding of how well these tools perform on other, less well-characterized, taxa. Using high-quality assemblies as ground truth, we benchmarked 12 plasmid detection tools (which identify plasmid contigs in assemblies) and four plasmid reconstruction tools (which group contigs from the same plasmid together). We tested their ability to characterize diverse plasmids from short-read assemblies representing a wide range of Enterobacterales and Enterococcus species, including newly discovered and poorly characterized species collected from nonhuman hosts. Plasmer, PlasmidEC, PlaScope, and gplas2 were the highest-scoring plasmid detection tools, performing well for both Enterobacterales and enterococci. The two major determinants of accurate plasmid detection were representation in plasmid databases\u2014with Enterobacterales plasmids being more easily detected than those from enterococci\u2014and assembly contiguity, which was also key for successful plasmid reconstruction. Gplas2 performed best for plasmid reconstruction; however, less than half of plasmids were perfectly reconstructed, suggesting that substantial room for improvement remains in this class of tools.<\/jats:p>","DOI":"10.1093\/bib\/bbaf589","type":"journal-article","created":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T04:26:41Z","timestamp":1762835201000},"source":"Crossref","is-referenced-by-count":7,"title":["Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species"],"prefix":"10.1093","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7219-0478","authenticated-orcid":false,"given":"Marco","family":"Teixeira","sequence":"first","affiliation":[{"name":"Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,","place":["United States"]},{"name":"Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology , Van Mourik Broekmanweg 6, Delft 2628 XE, Zuid Holland ,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7194-4322","authenticated-orcid":false,"given":"C\u00e9lia","family":"Souque","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School , 10 Shattuck St, Boston, MA 02115 ,","place":["United States"]},{"name":"Laboratory of Systems Pharmacology, Harvard Medical School , 200 Longwood Ave, Boston, MA 02115 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9132-7249","authenticated-orcid":false,"given":"Colin J","family":"Worby","sequence":"additional","affiliation":[{"name":"Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Terrance","family":"Shea","sequence":"additional","affiliation":[{"name":"Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0562-9735","authenticated-orcid":false,"given":"Nicoletta","family":"Commins","sequence":"additional","affiliation":[{"name":"Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5511-8717","authenticated-orcid":false,"given":"Joshua T","family":"Smith","sequence":"additional","affiliation":[{"name":"Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-9221-4556","authenticated-orcid":false,"given":"Arjun M","family":"Miklos","sequence":"additional","affiliation":[{"name":"Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7205-7431","authenticated-orcid":false,"given":"Thomas","family":"Abeel","sequence":"additional","affiliation":[{"name":"Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,","place":["United States"]},{"name":"Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology , Van Mourik Broekmanweg 6, Delft 2628 XE, Zuid Holland ,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7857-9145","authenticated-orcid":false,"given":"Ashlee M","family":"Earl","sequence":"additional","affiliation":[{"name":"Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3800-0714","authenticated-orcid":false,"given":"Abigail L","family":"Manson","sequence":"additional","affiliation":[{"name":"Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard , 415 Main St, Cambridge, MA 02142 ,","place":["United 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