{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T07:03:04Z","timestamp":1788850984711,"version":"build-2803163510"},"reference-count":61,"publisher":"Microbiology Society","issue":"11","license":[{"start":{"date-parts":[[2018,11,1]],"date-time":"2018-11-01T00:00:00Z","timestamp":1541030400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,11,1]]},"abstract":"<jats:p>\n                    The genome of\n                    <jats:italic>Bordetella pertussis<\/jats:italic>\n                    is complex, with high G+C content and many repeats, each longer than 1000\u2009bp. Long-read sequencing offers the opportunity to produce single-contig\n                    <jats:italic>B. pertussis<\/jats:italic>\n                    assemblies using sequencing reads which are longer than the repetitive sections, with the potential to reveal genomic features which were previously unobservable in multi-contig assemblies produced by short-read sequencing alone. We used an R9.4 MinION flow cell and barcoding to sequence five\n                    <jats:italic>B. pertussis<\/jats:italic>\n                    strains in a single sequencing run. We then trialled combinations of the many nanopore user community-built long-read analysis tools to establish the current optimal assembly pipeline for\n                    <jats:italic>B. pertussis<\/jats:italic>\n                    genome sequences. This pipeline produced closed genome sequences for four strains, allowing visualization of inter-strain genomic rearrangement. Read mapping to the Tohama I reference genome suggests that the remaining strain contains an ultra-long duplicated region (almost 200\u2009kbp), which was not resolved by our pipeline; further investigation also revealed that a second strain that was seemingly resolved by our pipeline may contain an even longer duplication, albeit in a small subset of cells. We have therefore demonstrated the ability to resolve the structure of several\n                    <jats:italic>B. pertussis<\/jats:italic>\n                    strains per single barcoded nanopore flow cell, but the genomes with highest complexity (e.g. very large duplicated regions) remain only partially resolved using the standard library preparation and will require an alternative library preparation method. For full strain characterization, we recommend hybrid assembly of long and short reads together; for comparison of genome arrangement, assembly using long reads alone is sufficient.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.000234","type":"journal-article","created":{"date-parts":[[2018,11,21]],"date-time":"2018-11-21T11:17:44Z","timestamp":1542799064000},"source":"Crossref","is-referenced-by-count":22,"title":["Resolving the complex Bordetella pertussis genome using barcoded nanopore sequencing"],"prefix":"10.1099","volume":"4","author":[{"given":"Natalie","family":"Ring","sequence":"first","affiliation":[{"name":"1\u200bDepartment of Biology and Biochemistry and the Milner Centre for Evolution, University of Bath, Bath, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan S.","family":"Abrahams","sequence":"additional","affiliation":[{"name":"1\u200bDepartment of Biology and Biochemistry and the Milner Centre for Evolution, University of Bath, Bath, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miten","family":"Jain","sequence":"additional","affiliation":[{"name":"2\u200bUC Santa Cruz Genomics Institute, 1156 High Street, Santa Cruz, CA 95064, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hugh","family":"Olsen","sequence":"additional","affiliation":[{"name":"2\u200bUC Santa Cruz Genomics Institute, 1156 High Street, Santa Cruz, CA 95064, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew","family":"Preston","sequence":"additional","affiliation":[{"name":"1\u200bDepartment of Biology and Biochemistry and the Milner Centre for Evolution, University of Bath, Bath, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Bagby","sequence":"additional","affiliation":[{"name":"1\u200bDepartment of Biology and Biochemistry and the Milner Centre for Evolution, University of Bath, Bath, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jit491"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1097\/MOP.0000000000000139"},{"key":"R3","volume-title":"Is the Circulating Uk Bordetella Pertussis Population Evolving to Evade Vaccine-Induced Immunity?","author":"Sealey","year":"2015"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiu001"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01339-14"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01074-14"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiu665"},{"key":"R8","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01189-14"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jis178"},{"key":"R10","doi-asserted-by":"publisher","DOI":"10.3201\/eid2004.131478"},{"key":"R11","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2474"},{"key":"R12","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.3009845"},{"key":"R13","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2014.11.014"},{"key":"R14","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3444"},{"key":"R15","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000132"},{"key":"R16","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky726"},{"key":"R17","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.4060"},{"key":"R18","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.4109"},{"key":"R19","doi-asserted-by":"publisher","DOI":"10.1038\/nature07517"},{"key":"R20","doi-asserted-by":"publisher","DOI":"10.1111\/1574-6976.12067"},{"key":"R21","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00036-16"},{"key":"R22","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00806-16"},{"key":"R23","doi-asserted-by":"publisher","DOI":"10.1038\/ng1227"},{"key":"R24","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro886"},{"key":"R25","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0000904"},{"key":"R26","doi-asserted-by":"publisher","DOI":"10.1016\/j.micinf.2006.04.014"},{"key":"R27","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/gix001"},{"key":"R28","article-title":"Multiplexed nanopore sequencing of HLA-B locus in M\u0101ori and Polynesian samples","author":"Ton","year":"2017","journal-title":"bioRxiv"},{"key":"R29","article-title":"Real-time DNA barcoding in a remote rainforest using nanopore sequencing","author":"Pomerantz","year":"2017","journal-title":"bioRxiv"},{"key":"R30","doi-asserted-by":"publisher","DOI":"10.1038\/nature16996"},{"key":"R31","article-title":"Extreme metagenomics using nanopore DNA sequencing: a field report from Svalbard 78 N","author":"Edwards","year":"2016","journal-title":"bioRxiv"},{"key":"R32","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000086"},{"key":"R33","doi-asserted-by":"publisher","DOI":"10.1101\/gr.089532.108"},{"key":"R34","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"R35","article-title":"Calculate length of all sequences in an multi-fasta file","year":"2014"},{"key":"R36","article-title":"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM","author":"Li","year":"2013","journal-title":"arXiv"},{"key":"R37","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"R38","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1604560113"},{"key":"R39","doi-asserted-by":"publisher","DOI":"10.1101\/gr.215087.116"},{"key":"R40","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw152"},{"key":"R41","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005595"},{"key":"R42","doi-asserted-by":"publisher","DOI":"10.1101\/gr.214270.116"},{"key":"R43","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0112963"},{"key":"R44","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"R45","article-title":"Comparison of Oxford Nanopore basecalling tools","author":"Wick","year":"2018"},{"key":"R46","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt086"},{"key":"R47","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv351"},{"key":"R48","article-title":"A simple test for uncorrected insertions and deletions (indels) in bacterial genomes","author":"Watson","year":"2018","journal-title":"Opiniomics"},{"key":"R49","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu153"},{"key":"R50","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0011147"},{"key":"R51","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/28.1.45"},{"key":"R52","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00869-17"},{"key":"R53","doi-asserted-by":"publisher","DOI":"10.1128\/genomeA.01404-16"},{"key":"R54","article-title":"Whale watching with BulkVis: a graphical viewer for Oxford Nanopore bulk fast5 files","author":"Payne","year":"2018","journal-title":"bioRxiv"},{"key":"R55","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02484-07"},{"key":"R56","article-title":"Mind the gaps - ignoring errors in long read assemblies critically affects protein prediction","author":"Watson","year":"2018","journal-title":"bioRXiv"},{"key":"R57","doi-asserted-by":"publisher","DOI":"10.1016\/j.gpb.2016.05.004"},{"key":"R58","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbp026"},{"key":"R59","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giy037"},{"key":"R60","article-title":"Clive G Brown: CTO plenary from London Calling","year":"2018"},{"key":"R61","doi-asserted-by":"publisher","DOI":"10.1101\/gr.213405.116"}],"container-title":["Microbial Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.000234?crawler=true&mimetype=application\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,15]],"date-time":"2023-12-15T08:19:48Z","timestamp":1702628388000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.000234"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,11,1]]},"references-count":61,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2018,11,1]]}},"URL":"https:\/\/doi.org\/10.1099\/mgen.0.000234","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/381640","asserted-by":"object"}]},"ISSN":["2057-5858"],"issn-type":[{"value":"2057-5858","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,11,1]]}}}