{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T18:50:44Z","timestamp":1790707844998,"version":"4.1.0"},"reference-count":34,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2021,6,7]],"date-time":"2021-06-07T00:00:00Z","timestamp":1623024000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2021,6,7]],"date-time":"2021-06-07T00:00:00Z","timestamp":1623024000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100013297","name":"Eurostars","doi-asserted-by":"publisher","award":["E! 10959"],"award-info":[{"award-number":["E! 10959"]}],"id":[{"id":"10.13039\/100013297","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Microbiol"],"published-print":{"date-parts":[[2021,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Bacterial plasmids often carry antibiotic resistance genes and are a significant factor in the spread of antibiotic resistance. The ability to completely assemble plasmid sequences would facilitate the localization of antibiotic resistance genes, the identification of genes that promote plasmid transmission and the accurate tracking of plasmid mobility. However, the complete assembly of plasmid sequences using the currently most widely used sequencing platform (Illumina-based sequencing) is restricted due to the generation of short sequence lengths. The long-read Oxford Nanopore Technologies (ONT) sequencing platform overcomes this limitation. Still, the assembly of plasmid sequence data remains challenging due to software incompatibility with long-reads and the error rate generated using ONT sequencing. Bioinformatics pipelines have been developed for ONT-generated sequencing but require computational skills that frequently are beyond the abilities of scientific researchers. To overcome this challenge, the authors developed \u2018WeFaceNano\u2019, a user-friendly Web interFace for rapid assembly and analysis of plasmid DNA sequences generated using the ONT platform. WeFaceNano includes: a read statistics report; two assemblers (Miniasm and Flye); BLAST searching; the detection of antibiotic resistance- and replicon genes and several plasmid visualizations. A user-friendly interface displays the main features of WeFaceNano and gives access to the analysis tools.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Publicly available ONT sequence data of 21 plasmids were used to validate WeFaceNano, with plasmid assemblages and anti-microbial resistance gene detection being concordant with the published results. Interestingly, the \u201cFlye\u201d assembler with \u201cmeta\u201d settings generated the most complete plasmids.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>WeFaceNano is a user-friendly open-source software pipeline suitable for accurate plasmid assembly and the detection of anti-microbial resistance genes in (clinical) samples where multiple plasmids can be present.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12866-021-02225-y","type":"journal-article","created":{"date-parts":[[2021,6,7]],"date-time":"2021-06-07T13:07:12Z","timestamp":1623071232000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["WeFaceNano: a user-friendly pipeline for complete ONT sequence assembly and detection of antibiotic resistance in multi-plasmid bacterial isolates"],"prefix":"10.1186","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7659-1917","authenticated-orcid":false,"given":"Astrid P.","family":"Heikema","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rick","family":"Jansen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saskia D.","family":"Hiltemann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John P.","family":"Hays","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew P.","family":"Stubbs","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,6,7]]},"reference":[{"issue":"2","key":"2225_CR1","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1007\/s10142-015-0433-4","volume":"15","author":"M Land","year":"2015","unstructured":"Land M, Hauser L, Jun SR, Nookaew I, Leuze MR, Ahn TH, et al. Insights from 20 years of bacterial genome sequencing. Funct Integr Genomics. 2015;15(2):141\u201361. https:\/\/doi.org\/10.1007\/s10142-015-0433-4.","journal-title":"Funct Integr Genomics"},{"issue":"1","key":"2225_CR2","doi-asserted-by":"publisher","first-page":"2101","DOI":"10.1038\/srep02101","volume":"3","author":"K Han","year":"2013","unstructured":"Han K, Li ZF, Peng R, Zhu LP, Zhou T, Wang LG, et al. Extraordinary expansion of a Sorangium cellulosum genome from an alkaline milieu. Sci Rep. 2013;3(1):2101. https:\/\/doi.org\/10.1038\/srep02101.","journal-title":"Sci Rep"},{"key":"2225_CR3","unstructured":"NCBI Blast Executables https:\/\/ftp.ncbi.nih.gov\/blast\/executables\/blast+\/2.9.0\/. Accessed 11 Mar\u00a02019."},{"issue":"1","key":"2225_CR4","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1128\/BR.40.1.168-189.1976","volume":"40","author":"RP Novick","year":"1976","unstructured":"Novick RP, Clowes RC, Cohen SN, Curtiss R 3rd, Datta N, Falkow S. Uniform nomenclature for bacterial plasmids: a proposal. Bacteriol Rev. 1976;40(1):168\u201389. https:\/\/doi.org\/10.1128\/BR.40.1.168-189.1976.","journal-title":"Bacteriol Rev"},{"key":"2225_CR5","unstructured":"Plasmid Database. http:\/\/gigadb.org\/dataset\/view\/id\/100387\/Sample_page\/2\/File_sort\/format_id."},{"key":"2225_CR6","doi-asserted-by":"publisher","first-page":"1479","DOI":"10.3389\/fmicb.2017.01479","volume":"8","author":"R Diaz-Orejas","year":"2017","unstructured":"Diaz-Orejas R, Espinosa M, Yeo CC. The importance of the expendable: toxin-antitoxin genes in plasmids and chromosomes. Front Microbiol. 2017;8:1479. https:\/\/doi.org\/10.3389\/fmicb.2017.01479.","journal-title":"Front Microbiol"},{"key":"2225_CR7","unstructured":"NCBI Database Genome Information Prokaryotes. https:\/\/www.ncbi.nlm.nih.gov\/genome\/browse#!\/prokaryotes\/. Accessed Feb\u00a02020."},{"issue":"6","key":"2225_CR8","doi-asserted-by":"publisher","first-page":"2157","DOI":"10.1007\/s00253-010-2671-7","volume":"87","author":"PH Oliveira","year":"2010","unstructured":"Oliveira PH, Prather KJ, Prazeres DM, Monteiro GA. Analysis of DNA repeats in bacterial plasmids reveals the potential for recurrent instability events. Appl Microbiol Biotechnol. 2010;87(6):2157\u201367. https:\/\/doi.org\/10.1007\/s00253-010-2671-7.","journal-title":"Appl Microbiol Biotechnol"},{"issue":"5","key":"2225_CR9","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1111\/dgd.12608","volume":"61","author":"N Kono","year":"2019","unstructured":"Kono N, Arakawa K. Nanopore sequencing: review of potential applications in functional genomics. Develop Growth Differ. 2019;61(5):316\u201326. https:\/\/doi.org\/10.1111\/dgd.12608.","journal-title":"Develop Growth Differ"},{"issue":"14","key":"2225_CR10","doi-asserted-by":"publisher","first-page":"2103","DOI":"10.1093\/bioinformatics\/btw152","volume":"32","author":"H Li","year":"2016","unstructured":"Li H. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics. 2016;32(14):2103\u201310. https:\/\/doi.org\/10.1093\/bioinformatics\/btw152.","journal-title":"Bioinformatics."},{"issue":"5","key":"2225_CR11","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1101\/gr.215087.116","volume":"27","author":"S Koren","year":"2017","unstructured":"Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 2017;27(5):722\u201336. https:\/\/doi.org\/10.1101\/gr.215087.116.","journal-title":"Genome Res"},{"key":"2225_CR12","unstructured":"PlasmidFinder Database. https:\/\/bitbucket.org\/genomicepidemiology\/plasmidfinder\/src\/master\/. Accessed 07 Feb\u00a02020."},{"key":"2225_CR13","unstructured":"WeFaceNano Software. https:\/\/github.com\/ErasmusMC-Bioinformatics\/WeFaceNano."},{"issue":"15","key":"2225_CR14","doi-asserted-by":"publisher","first-page":"2666","DOI":"10.1093\/bioinformatics\/bty149","volume":"34","author":"W De Coster","year":"2018","unstructured":"De Coster W, D'Hert S, Schultz DT, Cruts M, Van Broeckhoven C. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics. 2018;34(15):2666\u20139. https:\/\/doi.org\/10.1093\/bioinformatics\/bty149.","journal-title":"Bioinformatics."},{"key":"2225_CR15","unstructured":"Nanoplot Software. https:\/\/github.com\/wdecoster\/NanoPlot. Accessed 29 Jan\u00a02019."},{"key":"2225_CR16","unstructured":"A\u00a0representative overview of a WeFaceNano report.\u00a0The report contains raw read statistics and analysis results\u00a0of the RB04\u00a0sample.\u00a0https:\/\/erasmusmc-bioinformatics.github.io\/WeFaceNano\/. Accessed 20 Apr\u00a02021."},{"key":"2225_CR17","unstructured":"Porechop Software. https:\/\/github.com\/rrwick\/Porechop. Accessed 19 Oct\u00a02018."},{"issue":"18","key":"2225_CR18","doi-asserted-by":"publisher","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","volume":"34","author":"H Li","year":"2018","unstructured":"Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018;34(18):3094\u2013100. https:\/\/doi.org\/10.1093\/bioinformatics\/bty191.","journal-title":"Bioinformatics."},{"key":"2225_CR19","unstructured":"Minimap Software. https:\/\/github.com\/rrwick\/Porechop. Accessed 10 Jan\u00a02019."},{"issue":"1","key":"2225_CR20","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1093\/bioinformatics\/btt310","volume":"30","author":"R Chikhi","year":"2014","unstructured":"Chikhi R, Medvedev P. Informed and automated k-mer size selection for genome assembly. Bioinformatics. 2014;30(1):31\u20137. https:\/\/doi.org\/10.1093\/bioinformatics\/btt310.","journal-title":"Bioinformatics."},{"key":"2225_CR21","unstructured":"KmerGenie Software. http:\/\/kmergenie.bx.psu.edu\/.\u00a0Accessed 22 Nov\u00a02018."},{"key":"2225_CR22","unstructured":"Miniasm Software. https:\/\/github.com\/lh3\/miniasm. Accessed 24 July 2018."},{"issue":"5","key":"2225_CR23","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1101\/gr.214270.116","volume":"27","author":"R Vaser","year":"2017","unstructured":"Vaser R, Sovic I, Nagarajan N, Sikic M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 2017;27(5):737\u201346. https:\/\/doi.org\/10.1101\/gr.214270.116.","journal-title":"Genome Res"},{"key":"2225_CR24","unstructured":"Racon Software. https:\/\/github.com\/isovic\/racon. Accessed 30 May 2019."},{"key":"2225_CR25","unstructured":"Flye Software. https:\/\/github.com\/fenderglass\/Flye. Accessed 07 Apr\u00a02019."},{"issue":"11","key":"2225_CR26","doi-asserted-by":"publisher","first-page":"1103","DOI":"10.1038\/s41592-020-00971-x","volume":"17","author":"M Kolmogorov","year":"2020","unstructured":"Kolmogorov M, Bickhart DM, Behsaz B, Gurevich A, Rayko M, Shin SB, et al. metaFlye: scalable long-read metagenome assembly using repeat graphs. Nat Methods. 2020;17(11):1103\u201310. https:\/\/doi.org\/10.1038\/s41592-020-00971-x.","journal-title":"Nat Methods"},{"issue":"20","key":"2225_CR27","doi-asserted-by":"publisher","first-page":"3350","DOI":"10.1093\/bioinformatics\/btv383","volume":"31","author":"RR Wick","year":"2015","unstructured":"Wick RR, Schultz MB, Zobel J, Holt KE. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics. 2015;31(20):3350\u20132. https:\/\/doi.org\/10.1093\/bioinformatics\/btv383.","journal-title":"Bioinformatics."},{"key":"2225_CR28","unstructured":"Bandage Software.\u00a0https:\/\/rrwick.github.io\/Bandage\/. Accessed 15 Dec\u00a02016."},{"issue":"7","key":"2225_CR29","doi-asserted-by":"publisher","first-page":"3895","DOI":"10.1128\/AAC.02412-14","volume":"58","author":"A Carattoli","year":"2014","unstructured":"Carattoli A, Zankari E, Garcia-Fernandez A, Voldby Larsen M, Lund O, Villa L, et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014;58(7):3895\u2013903. https:\/\/doi.org\/10.1128\/AAC.02412-14.","journal-title":"Antimicrob Agents Chemother"},{"key":"2225_CR30","unstructured":"PlasmidFinder Bitbucket Repository. https:\/\/bitbucket.org\/genomicepidemiology\/plasmidfinder_db\/src\/master\/. Accessed 07 Feb\u00a02020."},{"key":"2225_CR31","unstructured":"brigD3 Software. https:\/\/github.com\/esteinig\/BRIGAD3. Accessed 26 May 2019."},{"issue":"3","key":"2225_CR32","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/gigascience\/gix132","volume":"7","author":"R Li","year":"2018","unstructured":"Li R, Xie M, Dong N, Lin D, Yang X, Wong MHY, et al. Efficient generation of complete sequences of MDR-encoding plasmids by rapid assembly of MinION barcoding sequencing data. Gigascience. 2018;7(3):1\u20139. https:\/\/doi.org\/10.1093\/gigascience\/gix132.","journal-title":"Gigascience."},{"issue":"11","key":"2225_CR33","doi-asserted-by":"publisher","first-page":"2640","DOI":"10.1093\/jac\/dks261","volume":"67","author":"E Zankari","year":"2012","unstructured":"Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012;67(11):2640\u20134. https:\/\/doi.org\/10.1093\/jac\/dks261.","journal-title":"J Antimicrob Chemother"},{"issue":"5","key":"2225_CR34","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","volume":"37","author":"M Kolmogorov","year":"2019","unstructured":"Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019;37(5):540\u20136. https:\/\/doi.org\/10.1038\/s41587-019-0072-8.","journal-title":"Nat Biotechnol"}],"container-title":["BMC Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12866-021-02225-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12866-021-02225-y\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12866-021-02225-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,6,7]],"date-time":"2021-06-07T13:09:37Z","timestamp":1623071377000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcmicrobiol.biomedcentral.com\/articles\/10.1186\/s12866-021-02225-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,6,7]]},"references-count":34,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2021,12]]}},"alternative-id":["2225"],"URL":"https:\/\/doi.org\/10.1186\/s12866-021-02225-y","relation":{},"ISSN":["1471-2180"],"issn-type":[{"value":"1471-2180","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,6,7]]},"assertion":[{"value":"4 May 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 May 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 June 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"171"}}