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MasterOfPores: A workflow for the analysis of Oxford nanopore direct RNA sequencing datasets

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dc.contributor.author Cozzuto, Luca
dc.contributor.author Liu, Huanle
dc.contributor.author Pryszcz, Leszek Piotr, 1985-
dc.contributor.author Hermoso Pulido, Antonio
dc.contributor.author Delgado-Tejedor, Anna
dc.contributor.author Ponomarenko, Julia
dc.contributor.author Novoa, Eva Maria
dc.date.accessioned 2020-05-07T11:02:55Z
dc.date.available 2020-05-07T11:02:55Z
dc.date.issued 2020
dc.identifier.citation Cozzuto L, Liu H, Pryszcz LP, Pulido TH, Delgado-Tejedor A, Ponomarenko J et al. MasterOfPores: A workflow for the analysis of Oxford nanopore direct RNA sequencing datasets. Front Genet. 2020 Mar 17; 11:211. DOI: 10.3389/fgene.2020.00211
dc.identifier.issn 1664-8021
dc.identifier.uri http://hdl.handle.net/10230/44450
dc.description.abstract The direct RNA sequencing platform offered by Oxford Nanopore Technologies allows for direct measurement of RNA molecules without the need of conversion to complementary DNA, fragmentation or amplification. As such, it is virtually capable of detecting any given RNA modification present in the molecule that is being sequenced, as well as provide polyA tail length estimations at the level of individual RNA molecules. Although this technology has been publicly available since 2017, the complexity of the raw Nanopore data, together with the lack of systematic and reproducible pipelines, have greatly hindered the access of this technology to the general user. Here we address this problem by providing a fully benchmarked workflow for the analysis of direct RNA sequencing reads, termed MasterOfPores. The pipeline starts with a pre-processing module, which converts raw current intensities into multiple types of processed data including FASTQ and BAM, providing metrics of the quality of the run, quality-filtering, demultiplexing, base-calling and mapping. In a second step, the pipeline performs downstream analyses of the mapped reads, including prediction of RNA modifications and estimation of polyA tail lengths. Four direct RNA MinION sequencing runs can be fully processed and analyzed in 10 h on 100 CPUs. The pipeline can also be executed in GPU locally or in the cloud, decreasing the run time fourfold. The software is written using the NextFlow framework for parallelization and portability, and relies on Linux containers such as Docker and Singularity for achieving better reproducibility. The MasterOfPores workflow can be executed on any Unix-compatible OS on a computer, cluster or cloud without the need of installing any additional software or dependencies, and is freely available in Github (https://github.com/biocorecrg/master_of_pores). This workflow simplifies direct RNA sequencing data analyses, facilitating the study of the (epi)transcriptome at single molecule resolution.
dc.description.sponsorship This work was partly supported by the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) (PGC2018-098152-A-100 to EN) and by the Australian Research Council (DP180103571 to EN). LP was supported by funding from the European Union’s H2020 Research and Innovation Programme under Marie Skłodowska-Curie grant agreement no. 754422
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Frontiers Media
dc.relation.ispartof Frontiers in Genetics. 2020 Mar 17; 11:211
dc.rights © 2020 by Luca Cozzuto et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.subject.other Genètica
dc.subject.other Seqüència de nucleòtids
dc.subject.other Nanotecnologia
dc.title MasterOfPores: A workflow for the analysis of Oxford nanopore direct RNA sequencing datasets
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.3389/fgene.2020.00211
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/754422
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PGC2018-098152-A-100
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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