دورية أكاديمية
MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets.
| العنوان: | MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets. |
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| المؤلفون: | Cozzuto L; Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain., Liu H; Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain., Pryszcz LP; Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.; International Institute of Molecular and Cell Biology, Warsaw, Poland., Pulido TH; Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain., Delgado-Tejedor A; Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.; Universitat Pompeu Fabra, Barcelona, Spain., Ponomarenko J; Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.; Universitat Pompeu Fabra, Barcelona, Spain., Novoa EM; Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.; Universitat Pompeu Fabra, Barcelona, Spain.; Department of Neuroscience, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.; St Vincent's Clinical School, UNSW Sydney, Darlinghurst, NSW, Australia. |
| المصدر: | Frontiers in genetics [Front Genet] 2020 Mar 17; Vol. 11, pp. 211. Date of Electronic Publication: 2020 Mar 17 (Print Publication: 2020). |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Frontiers Research Foundation Country of Publication: Switzerland NLM ID: 101560621 Publication Model: eCollection Cited Medium: Print ISSN: 1664-8021 (Print) Linking ISSN: 16648021 NLM ISO Abbreviation: Front Genet Subsets: PubMed not MEDLINE |
| أسماء مطبوعة: | Original Publication: Lausanne : Frontiers Research Foundation. |
| مستخلص: | 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. (Copyright © 2020 Cozzuto, Liu, Pryszcz, Pulido, Delgado-Tejedor, Ponomarenko and Novoa.) |
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| فهرسة مساهمة: | Keywords: Docker; Nextflow; direct RNA sequencing; nanopore; singularity |
| تواريخ الأحداث: | Date Created: 20200408 Latest Revision: 20240328 |
| رمز التحديث: | 20240329 |
| مُعرف محوري في PubMed: | PMC7089958 |
| DOI: | 10.3389/fgene.2020.00211 |
| PMID: | 32256520 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 1664-8021 |
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| DOI: | 10.3389/fgene.2020.00211 |