Accurate isoform discovery with IsoQuant using long reads

Annotating newly sequenced genomes and determining alternative isoforms from long-read RNA data are complex and incompletely solved problems. Here we present IsoQuant—a computational tool using intron graphs that accurately reconstructs transcripts both with and without reference genome annotation....

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Detalles Bibliográficos
Autores principales: Prjibelski, Andrey D., Mikheenko, Alla, Joglekar, Anoushka, Smetanin, Alexander, Jarroux, Julien, Lapidus, Alla L., Tilgner, Hagen U.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group US 2023
Materias:
Brief Communication
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10344776/
https://www.ncbi.nlm.nih.gov/pubmed/36593406
http://dx.doi.org/10.1038/s41587-022-01565-y
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author Prjibelski, Andrey D.
Mikheenko, Alla
Joglekar, Anoushka
Smetanin, Alexander
Jarroux, Julien
Lapidus, Alla L.
Tilgner, Hagen U.
author_facet Prjibelski, Andrey D.
Mikheenko, Alla
Joglekar, Anoushka
Smetanin, Alexander
Jarroux, Julien
Lapidus, Alla L.
Tilgner, Hagen U.
author_sort Prjibelski, Andrey D.
collection PubMed
description Annotating newly sequenced genomes and determining alternative isoforms from long-read RNA data are complex and incompletely solved problems. Here we present IsoQuant—a computational tool using intron graphs that accurately reconstructs transcripts both with and without reference genome annotation. For novel transcript discovery, IsoQuant reduces the false-positive rate fivefold and 2.5-fold for Oxford Nanopore reference-based or reference-free mode, respectively. IsoQuant also improves performance for Pacific Biosciences data.
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spelling pubmed-103447762023-07-15 Accurate isoform discovery with IsoQuant using long reads Prjibelski, Andrey D. Mikheenko, Alla Joglekar, Anoushka Smetanin, Alexander Jarroux, Julien Lapidus, Alla L. Tilgner, Hagen U. Nat Biotechnol Brief Communication Annotating newly sequenced genomes and determining alternative isoforms from long-read RNA data are complex and incompletely solved problems. Here we present IsoQuant—a computational tool using intron graphs that accurately reconstructs transcripts both with and without reference genome annotation. For novel transcript discovery, IsoQuant reduces the false-positive rate fivefold and 2.5-fold for Oxford Nanopore reference-based or reference-free mode, respectively. IsoQuant also improves performance for Pacific Biosciences data. Nature Publishing Group US 2023-01-02 2023 /pmc/articles/PMC10344776/ /pubmed/36593406 http://dx.doi.org/10.1038/s41587-022-01565-y Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Brief Communication
Prjibelski, Andrey D.
Mikheenko, Alla
Joglekar, Anoushka
Smetanin, Alexander
Jarroux, Julien
Lapidus, Alla L.
Tilgner, Hagen U.
Accurate isoform discovery with IsoQuant using long reads
title Accurate isoform discovery with IsoQuant using long reads
title_full Accurate isoform discovery with IsoQuant using long reads
title_fullStr Accurate isoform discovery with IsoQuant using long reads
title_full_unstemmed Accurate isoform discovery with IsoQuant using long reads
title_short Accurate isoform discovery with IsoQuant using long reads
title_sort accurate isoform discovery with isoquant using long reads
topic Brief Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10344776/
https://www.ncbi.nlm.nih.gov/pubmed/36593406
http://dx.doi.org/10.1038/s41587-022-01565-y
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