RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing

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  • dc.contributor.author Rubia, Ivan de la
  • dc.contributor.author Srivastava, Akanksha
  • dc.contributor.author Xue, Wenjing
  • dc.contributor.author Indi, Joel A.
  • dc.contributor.author Carbonell Sala, Silvia
  • dc.contributor.author Lagarde, Julien
  • dc.contributor.author Albà Soler, Mar
  • dc.contributor.author Eyras Jiménez, Eduardo
  • dc.date.accessioned 2022-11-02T07:28:43Z
  • dc.date.available 2022-11-02T07:28:43Z
  • dc.date.issued 2022
  • dc.description.abstract Nanopore sequencing enables the efficient and unbiased measurement of transcriptomes. Current methods for transcript identification and quantification rely on mapping reads to a reference genome, which precludes the study of species with a partial or missing reference or the identification of disease-specific transcripts not readily identifiable from a reference. We present RATTLE, a tool to perform reference-free reconstruction and quantification of transcripts using only Nanopore reads. Using simulated data and experimental data from isoform spike-ins, human tissues, and cell lines, we show that RATTLE accurately determines transcript sequences and their abundances, and shows good scalability with the number of transcripts.
  • dc.description.sponsorship This work was funded by the Spanish Agencia Estatal de Investigación with grants BFU2015-65235-P (to M.M. Alba), by the Spanish Ministerio de Ciencia, Innovación y Universidades with grants BIO2017-85364-R (to E. Eyras), PGC2018-094091-B-I00 (to M.M. Alba), and PRE2018-083413 (to I. de la Rubia), by the Catalan Government (AGAUR) with grant SGR2017-1020 (to M.M. Alba), and by the Australian Research Council (ARC) with grants DP210102385 and DP220101352 (to E. Eyras).
  • dc.format.mimetype application/pdf
  • dc.identifier.citation de la Rubia I, Srivastava A, Xue W, Indi JA, Carbonell-Sala S, Lagarde J, Albà MM, Eyras E. RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing. Genome Biol. 2022 Jul 8;23(1):153. DOI: 10.1186/s13059-022-02715-w
  • dc.identifier.doi http://dx.doi.org/10.1186/s13059-022-02715-w
  • dc.identifier.issn 1474-7596
  • dc.identifier.uri http://hdl.handle.net/10230/54645
  • dc.language.iso eng
  • dc.publisher BioMed Central
  • dc.relation.ispartof Genome Biol. 2022 Jul 8;23(1):153
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2015-65235-P
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/BIO2017-85364-R
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PGC2018-094091-B-I00
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PRE2018-083413
  • dc.rights © The Author(s) 2022. 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.title RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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