دورية أكاديمية
ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data.
| العنوان: | ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data. |
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| المؤلفون: | Pryszcz LP; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain.; International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland., Novoa EM; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain.; Universitat Pompeu Fabra (UPF), Barcelona, Spain. |
| المصدر: | Bioinformatics (Oxford, England) [Bioinformatics] 2021 Dec 22; Vol. 38 (1), pp. 257-260. |
| نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't |
| اللغة: | English |
| بيانات الدورية: | Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: Oxford : Oxford University Press, c1998- |
| مواضيع طبية MeSH: | Nanopore Sequencing* , Nanopores*, Sequence Analysis, DNA/methods ; Software ; DNA ; RNA ; High-Throughput Nucleotide Sequencing |
| مستخلص: | Motivation: DNA and RNA modifications can now be identified using nanopore sequencing. However, we currently lack a flexible software to efficiently encode, store, analyze and visualize DNA and RNA modification data. Results: Here, we present ModPhred, a versatile toolkit that facilitates DNA and RNA modification analysis from nanopore sequencing reads in a user-friendly manner. ModPhred integrates probabilistic DNA and RNA modification information within the FASTQ and BAM file formats, can be used to encode multiple types of modifications simultaneously, and its output can be easily coupled to genomic track viewers, facilitating the visualization and analysis of DNA and RNA modification information in individual reads in a simple and computationally efficient manner. Availability and Implementation: ModPhred is available at https://github.com/novoalab/modPhred, is implemented in Python3, and is released under an MIT license. Docker images with all dependencies preinstalled are also provided. Supplementary Information: Supplementary data are available at Bioinformatics online. (© The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.) |
| معلومات مُعتمدة: | 754422 European Union's H2020 research and innovation programme under Marie Sklodowska-Curie; PGC2018-098152-A-100 Spanish Ministry of Economy, Industry and Competitiveness (MEIC); Spanish Ministry of Science and Innovation to the EMBL partnership; Centro de Excelencia Severo Ochoa and CERCA Programme/Generalitat de Catalunya |
| المشرفين على المادة: | 9007-49-2 (DNA) 63231-63-0 (RNA) |
| تواريخ الأحداث: | Date Created: 20210722 Date Completed: 20230202 Latest Revision: 20230207 |
| رمز التحديث: | 20240628 |
| DOI: | 10.1093/bioinformatics/btab539 |
| PMID: | 34293115 |
| قاعدة البيانات: | MEDLINE |
| تدمد: | 1367-4811 |
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| DOI: | 10.1093/bioinformatics/btab539 |