{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:33:59Z","timestamp":1772138039958,"version":"3.50.1"},"reference-count":59,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2020,7,16]],"date-time":"2020-07-16T00:00:00Z","timestamp":1594857600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Agence Nationale de la Recherche [ANRJCJC \u2013 WIRED]"},{"DOI":"10.13039\/501100018874","name":"Labex EpiGenMed","doi-asserted-by":"crossref","award":["ANR-10-LABX-12-01"],"award-info":[{"award-number":["ANR-10-LABX-12-01"]}],"id":[{"id":"10.13039\/501100018874","id-type":"DOI","asserted-by":"crossref"}]},{"name":"MUSE initiative [GECKO]"},{"name":"France G\u00e9nomique National infrastructure"},{"name":"Agence Nationale pour la Recherche","award":["ANR-10-INBS-09"],"award-info":[{"award-number":["ANR-10-INBS-09"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,12,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Long-read sequencing technologies are invaluable for determining complex RNA transcript architectures but are error-prone. Numerous \u2018hybrid correction\u2019 algorithms have been developed for genomic data that correct long reads by exploiting the accuracy and depth of short reads sequenced from the same sample. These algorithms are not suited for correcting more complex transcriptome sequencing data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We have created a novel reference-free algorithm called Transcript-level Aware Long-Read Correction (TALC) which models changes in RNA expression and isoform representation in a weighted De Bruijn graph to correct long reads from transcriptome studies. We show that transcript-level aware correction by TALC improves the accuracy of the whole spectrum of downstream RNA-seq applications and is thus necessary for transcriptome analyses that use long read technology.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>TALC is implemented in C++ and available at https:\/\/github.com\/lbroseus\/TALC.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa634","type":"journal-article","created":{"date-parts":[[2020,7,10]],"date-time":"2020-07-10T07:34:24Z","timestamp":1594366464000},"page":"5000-5006","source":"Crossref","is-referenced-by-count":15,"title":["TALC: Transcript-level Aware Long-read Correction"],"prefix":"10.1093","volume":"36","author":[{"given":"Lucile","family":"Broseus","sequence":"first","affiliation":[{"name":"Department of Genome Dynamics, Institut de G\u00e9n\u00e9tique Humaine, Centre National de la Recherche Scientifique (CNRS), Universit\u00e9 de Montpellier , Montpellier 34396, France"}]},{"given":"Aubin","family":"Thomas","sequence":"additional","affiliation":[{"name":"Department of Genome Dynamics, Institut de G\u00e9n\u00e9tique Humaine, Centre National de la Recherche Scientifique (CNRS), Universit\u00e9 de Montpellier , Montpellier 34396, France"}]},{"given":"Andrew J","family":"Oldfield","sequence":"additional","affiliation":[{"name":"Department of Genome Dynamics, Institut de G\u00e9n\u00e9tique Humaine, Centre National de la Recherche Scientifique (CNRS), Universit\u00e9 de Montpellier , Montpellier 34396, France"}]},{"given":"Dany","family":"Severac","sequence":"additional","affiliation":[{"name":"MGX-Montpellier GenomiX, c\/o Institut de G\u00e9nomique Fonctionnelle , Montpellier Cedex 5 34094, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6052-4178","authenticated-orcid":false,"given":"Emeric","family":"Dubois","sequence":"additional","affiliation":[{"name":"MGX-Montpellier GenomiX, c\/o Institut de G\u00e9nomique Fonctionnelle , Montpellier Cedex 5 34094, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8162-1439","authenticated-orcid":false,"given":"William","family":"Ritchie","sequence":"additional","affiliation":[{"name":"Department of Genome Dynamics, Institut de G\u00e9n\u00e9tique Humaine, Centre National de la Recherche Scientifique (CNRS), Universit\u00e9 de Montpellier , Montpellier 34396, France"}]}],"member":"286","published-online":{"date-parts":[[2020,7,16]]},"reference":[{"key":"2023062408113339200_btaa634-B1","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/s13059-020-1935-5","article-title":"Opportunities and challenges in long-read sequencing data analysis","volume":"21","author":"Amarasinghe","year":"2020","journal-title":"Genome Biol"},{"key":"2023062408113339200_btaa634-B2","doi-asserted-by":"crossref","first-page":"e46679","DOI":"10.1371\/journal.pone.0046679","article-title":"Improving PacBio long read accuracy by short read alignment","volume":"7","author":"Au","year":"2012","journal-title":"PLoS ONE"},{"key":"2023062408113339200_btaa634-B3","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1186\/s12859-017-1610-3","article-title":"HALC: high throughput algorithm for long read error correction","volume":"18","author":"Bao","year":"2017","journal-title":"BMC Bioinformatics"},{"key":"2023062408113339200_btaa634-B4","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1016\/j.tim.2019.01.010","article-title":"Long-read sequencing \u2013 a powerful tool in viral transcriptome research","volume":"27","author":"Boldogk\u0151i","year":"2019","journal-title":"Trends Microbiol"},{"key":"2023062408113339200_btaa634-B5","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1038\/sdata.2018.276","article-title":"Transcriptome-wide analysis of a baculovirus using nanopore sequencing","volume":"5","author":"Boldogk\u0151i","year":"2018","journal-title":"Sci. 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