{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T19:05:01Z","timestamp":1775329501958,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2023,3,24]],"date-time":"2023-03-24T00:00:00Z","timestamp":1679616000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union\u2019s Horizon 2020 Research and Innovation Programme"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,5,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Iso-Seq RNA long-read sequencing enables the identification of full-length transcripts and isoforms, removing the need for complex analysis such as transcriptome assembly. However, the raw sequencing data need to be processed in a series of steps before annotation is complete. Here, we present nf-core\/isoseq, a pipeline for automatic read processing and genome annotation. Following nf-core guidelines, the pipeline has few dependencies and can be run on any of platforms.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The pipeline is freely available online on the nf-core website (https:\/\/nf-co.re\/isoseq) and on GitHub (https:\/\/github.com\/nf-core\/isoseq) under MIT License (DOI: 10.5281\/zenodo.7116979).<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad150","type":"journal-article","created":{"date-parts":[[2023,3,24]],"date-time":"2023-03-24T14:06:30Z","timestamp":1679666790000},"source":"Crossref","is-referenced-by-count":24,"title":["nf-core\/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5116-4150","authenticated-orcid":false,"given":"S\u00e9bastien","family":"Guizard","sequence":"first","affiliation":[{"name":"The Roslin Institute and R(D)SVS, University of Edinburgh , Edinburgh EH25 9RG, United Kingdom"}]},{"given":"Katarzyna","family":"Miedzinska","sequence":"additional","affiliation":[{"name":"The Roslin Institute and R(D)SVS, University of Edinburgh , Edinburgh EH25 9RG, United Kingdom"}]},{"given":"Jacqueline","family":"Smith","sequence":"additional","affiliation":[{"name":"The Roslin Institute and R(D)SVS, University of Edinburgh , Edinburgh EH25 9RG, United Kingdom"}]},{"given":"Jonathan","family":"Smith","sequence":"additional","affiliation":[{"name":"The Roslin Institute and R(D)SVS, University of Edinburgh , Edinburgh EH25 9RG, United Kingdom"}]},{"given":"Richard I","family":"Kuo","sequence":"additional","affiliation":[{"name":"Wobble Genomics, University of Edinburgh , Edinburgh EH25 9RG, United Kingdom"}]},{"given":"Megan","family":"Davey","sequence":"additional","affiliation":[{"name":"The Roslin Institute and R(D)SVS, University of Edinburgh , Edinburgh EH25 9RG, United Kingdom"}]},{"given":"Alan","family":"Archibald","sequence":"additional","affiliation":[{"name":"The Roslin Institute and R(D)SVS, University of Edinburgh , Edinburgh EH25 9RG, United Kingdom"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4211-0358","authenticated-orcid":false,"given":"Mick","family":"Watson","sequence":"additional","affiliation":[{"name":"The Roslin Institute and R(D)SVS, University of Edinburgh , Edinburgh EH25 9RG, United Kingdom"}]}],"member":"286","published-online":{"date-parts":[[2023,3,24]]},"reference":[{"key":"2023052007035306800_btad150-B1","doi-asserted-by":"crossref","first-page":"1691","DOI":"10.1093\/bioinformatics\/btr174","article-title":"BamTools: a C++ API and toolkit for analyzing and managing BAM 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