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Methplotlib: analysis of modified nucleotides from nanopore sequencing.

ABSTRACT: SUMMARY:Modified nucleotides play a crucial role in gene expression regulation. Here, we describe methplotlib, a tool developed for the visualization of modified nucleotides detected from Oxford Nanopore Technologies sequencing platforms, together with additional scripts for statistical analysis of allele-specific modification within-subjects and differential modification frequency across subjects. AVAILABILITY AND IMPLEMENTATION:The methplotlib command-line tool is written in Python3, is compatible with Linux, Mac OS and the MS Windows 10 Subsystem for Linux and released under the MIT license. The source code can be found at https://github.com/wdecoster/methplotlib and can be installed from PyPI and bioconda. Our repository includes test data, and the tool is continuously tested at travis-ci.com. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.

SUBMITTER: De Coster W

PROVIDER: S-EPMC7214038 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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Methplotlib: analysis of modified nucleotides from nanopore sequencing.

De Coster Wouter W Stovner Endre Bakken EB Strazisar Mojca M

Bioinformatics (Oxford, England) 20200501 10

<h4>Summary</h4>Modified nucleotides play a crucial role in gene expression regulation. Here, we describe methplotlib, a tool developed for the visualization of modified nucleotides detected from Oxford Nanopore Technologies sequencing platforms, together with additional scripts for statistical analysis of allele-specific modification within-subjects and differential modification frequency across subjects.<h4>Availability and implementation</h4>The methplotlib command-line tool is written in Pyt ...[more]

PMID: 32053166

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