{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,4]],"date-time":"2026-10-04T21:22:02Z","timestamp":1791148922598,"version":"4.1.0"},"reference-count":59,"publisher":"American Society for Microbiology","issue":"7","license":[{"start":{"date-parts":[[2024,7,23]],"date-time":"2024-07-23T00:00:00Z","timestamp":1721692800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2024,7,23]],"date-time":"2024-07-23T00:00:00Z","timestamp":1721692800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000060","name":"HHS | NIH | National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01-AI170583"],"award-info":[{"award-number":["R01-AI170583"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"HHS | NIH | National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01-AI170583"],"award-info":[{"award-number":["R01-AI170583"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"HHS | NIH | National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01-AI152543"],"award-info":[{"award-number":["R01-AI152543"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"crossref","award":["FOR5200 DEEP-DV (443644894)"],"award-info":[{"award-number":["FOR5200 DEEP-DV (443644894)"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"crossref","award":["EXC 2155 (390874280)"],"award-info":[{"award-number":["EXC 2155 (390874280)"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mSystems"],"published-print":{"date-parts":[[2024,7,23]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Nanopore direct RNA sequencing (DRS) enables the capture and full-length sequencing of native RNAs, without recoding or amplification bias. Resulting data sets may be interrogated to define the identity and location of chemically modified ribonucleotides, as well as the length of poly(A) tails, on individual RNA molecules. The success of these analyses is highly dependent on the provision of high-resolution transcriptome annotations in combination with workflows that minimize misalignments and other analysis artifacts. Existing software solutions for generating high-resolution transcriptome annotations are poorly suited to small gene-dense genomes of viruses due to the challenge of identifying distinct transcript isoforms where alternative splicing and overlapping RNAs are prevalent. To resolve this, we identified key characteristics of DRS data sets that inform resulting read alignments and developed the nanopore guided annotation of transcriptome architectures (NAGATA) software package (\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/DepledgeLab\/NAGATA\" xlink:type=\"simple\">https:\/\/github.com\/DepledgeLab\/NAGATA<\/jats:ext-link>\n                      ). We demonstrate, using a combination of synthetic and original DRS data sets derived from adenoviruses, herpesviruses, coronaviruses, and human cells, that NAGATA outperforms existing transcriptome annotation software and yields a consistently high level of precision and recall when reconstructing both gene sparse and gene-dense transcriptomes. Finally, we apply NAGATA to generate the first high-resolution transcriptome annotation of the neglected pathogen human adenovirus type F41 (HAdV-41) for which we identify 77 distinct transcripts encoding at least 23 different proteins.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>The transcriptome of an organism denotes the full repertoire of encoded RNAs that may be expressed. This is critical to understanding the biology of an organism and for accurate transcriptomic and epitranscriptomic-based analyses. Annotating transcriptomes remains a complex task, particularly in small gene-dense organisms such as viruses which maximize their coding capacity through overlapping RNAs. To resolve this, we have developed a new software nanopore guided annotation of transcriptome architectures (NAGATA) which utilizes nanopore direct RNA sequencing (DRS) datasets to rapidly produce high-resolution transcriptome annotations for diverse viruses and other organisms.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/msystems.00505-24","type":"journal-article","created":{"date-parts":[[2024,7,2]],"date-time":"2024-07-02T06:16:20Z","timestamp":1719900980000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":10,"title":["Nanopore guided annotation of transcriptome architectures"],"prefix":"10.1128","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-1268-0427","authenticated-orcid":false,"given":"Jonathan S.","family":"Abebe","sequence":"first","affiliation":[{"name":"Department of Microbiology, New York University School of Medicine, New York, New York, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7001-5641","authenticated-orcid":false,"given":"Yasmine","family":"Alwie","sequence":"additional","affiliation":[{"name":"Institute of Virology, Hannover Medical School, Hannover, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-8512-9369","authenticated-orcid":false,"given":"Erik","family":"Fuhrmann","sequence":"additional","affiliation":[{"name":"Institute of Virology, Hannover Medical School, Hannover, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonas","family":"Leins","sequence":"additional","affiliation":[{"name":"Institute of Virology, Hannover Medical School, Hannover, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9501-5691","authenticated-orcid":false,"given":"Julia","family":"Mai","sequence":"additional","affiliation":[{"name":"Institute of Virology, Hannover Medical School, Hannover, Germany"},{"name":"Institute of Virology, University Medical Center, Albert-Ludwigs-University Freiburg, Freiburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-6046-6335","authenticated-orcid":false,"given":"Ruth","family":"Verstraten","sequence":"additional","affiliation":[{"name":"Institute of Virology, Hannover Medical School, Hannover, Germany"},{"name":"German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5744-7159","authenticated-orcid":false,"given":"Sabrina","family":"Schreiner","sequence":"additional","affiliation":[{"name":"Institute of Virology, Hannover Medical School, Hannover, Germany"},{"name":"Institute of Virology, University Medical Center, Albert-Ludwigs-University Freiburg, Freiburg, Germany"},{"name":"Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5016-4164","authenticated-orcid":false,"given":"Angus C.","family":"Wilson","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University School of Medicine, New York, New York, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4292-0599","authenticated-orcid":false,"given":"Daniel P.","family":"Depledge","sequence":"additional","affiliation":[{"name":"Department of Microbiology, New York University School of Medicine, New York, New York, USA"},{"name":"Institute of Virology, Hannover Medical School, Hannover, Germany"},{"name":"German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany"},{"name":"Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.biocel.2008.09.015"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01342-18"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.12688\/f1000research.10571.2"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4577"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3444"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1261\/rna.071332.119"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac274"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-021-00915-6"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-022-01513-3"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-022-01666-1"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-020-0849-9"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1010797"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1010084"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01568-20"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-08734-9"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-15992-5"},{"key":"e_1_3_4_18_2","doi-asserted-by":"publisher","unstructured":"Dong X Du MRM Gouil Q Tian L Jabbari JS Bowden R Baldoni PL Chen Y Smyth GK Amarasinghe SL Law CW Ritchie ME. 2023. Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures. Bioinformatics. doi:10.1101\/2022.07.22.501076","DOI":"10.1101\/2022.07.22.501076"},{"key":"e_1_3_4_19_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1910-1"},{"key":"e_1_3_4_20_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-023-01908-w"},{"key":"e_1_3_4_21_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-022-01565-y"},{"key":"e_1_3_4_22_2","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.20.3.365-372.1984"},{"key":"e_1_3_4_23_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-642-79586-2_12"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.1080\/21505594.2023.2242544"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-06003-w"},{"key":"e_1_3_4_26_2","doi-asserted-by":"publisher","DOI":"10.1101\/gad.348320.121"},{"key":"e_1_3_4_27_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.229102"},{"key":"e_1_3_4_28_2","doi-asserted-by":"publisher","DOI":"10.1002\/0471250953.bi1112s47"},{"key":"e_1_3_4_29_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.virusres.2010.12.018"},{"key":"e_1_3_4_30_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0702158104"},{"key":"e_1_3_4_31_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.260836.120"},{"key":"e_1_3_4_32_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty191"},{"key":"e_1_3_4_33_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"e_1_3_4_34_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.04.011"},{"key":"e_1_3_4_35_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1754"},{"key":"e_1_3_4_36_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-3578-9_16"},{"key":"e_1_3_4_37_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003118"},{"key":"e_1_3_4_38_2","doi-asserted-by":"crossref","unstructured":"Wickham H. 2016. ggplot2: Elegant Graphics for data analysis Springer-Verlag New York","DOI":"10.1007\/978-3-319-24277-4_9"},{"key":"e_1_3_4_39_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx364"},{"key":"e_1_3_4_40_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-19787-6"},{"key":"e_1_3_4_41_2","doi-asserted-by":"publisher","DOI":"10.15252\/embr.202256327"},{"key":"e_1_3_4_42_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-019-0617-2"},{"key":"e_1_3_4_43_2","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.49658"},{"key":"e_1_3_4_44_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab713"},{"key":"e_1_3_4_45_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-015-0557-5"},{"key":"e_1_3_4_46_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.45.1.185-191.1983"},{"key":"e_1_3_4_47_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41580-021-00432-z"},{"key":"e_1_3_4_48_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.78.16.8824-8834.2004"},{"key":"e_1_3_4_49_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.70.4.2658-2663.1996"},{"key":"e_1_3_4_50_2","doi-asserted-by":"publisher","DOI":"10.1016\/0042-6822(88)90639-3"},{"key":"e_1_3_4_51_2","doi-asserted-by":"publisher","DOI":"10.1016\/0042-6822(92)90761-D"},{"key":"e_1_3_4_52_2","doi-asserted-by":"publisher","DOI":"10.1016\/0042-6822(87)90080-8"},{"key":"e_1_3_4_53_2","doi-asserted-by":"publisher","DOI":"10.1016\/0378-1119(87)90034-5"},{"key":"e_1_3_4_54_2","doi-asserted-by":"publisher","DOI":"10.1016\/0042-6822(88)90662-9"},{"key":"e_1_3_4_55_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01869-20"},{"key":"e_1_3_4_56_2","doi-asserted-by":"publisher","DOI":"10.1016\/0092-8674(81)90145-8"},{"key":"e_1_3_4_57_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.156232.113"},{"key":"e_1_3_4_58_2","doi-asserted-by":"publisher","DOI":"10.1006\/geno.1996.0567"},{"key":"e_1_3_4_59_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac144"},{"key":"e_1_3_4_60_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-61779-292-2_11"}],"container-title":["mSystems"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/msystems.00505-24","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/msystems.00505-24","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,23]],"date-time":"2024-07-23T09:21:20Z","timestamp":1721726480000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/msystems.00505-24"}},"subtitle":[],"editor":[{"given":"Evelien M.","family":"Adriaenssens","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2024,7,23]]},"references-count":59,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2024,7,23]]}},"alternative-id":["10.1128\/msystems.00505-24"],"URL":"https:\/\/doi.org\/10.1128\/msystems.00505-24","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.04.02.587744","asserted-by":"object"}]},"ISSN":["2379-5077"],"issn-type":[{"value":"2379-5077","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,7,23]]},"assertion":[{"value":"2024-04-09","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-06-11","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-07-02","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00505-24"}}