Methplotlib: analysis of modified nucleotides from nanopore sequencing

Wouter De Coster; Endre Bakken Stovner; Mojca Strazisar

doi:10.1093/bioinformatics/btaa093

Methplotlib: analysis of modified nucleotides from nanopore sequencing

Bioinformatics. 2020 May 1;36(10):3236-3238. doi: 10.1093/bioinformatics/btaa093.

Authors

Wouter De Coster¹, Endre Bakken Stovner^{2

3}, Mojca Strazisar¹

Affiliations

¹ VIB, Center for Molecular Neurology, Antwerp 2610, Belgium.
² Department of Computer Science, Norwegian University of Science and Technology, Trondheim 7013, Norway.
³ Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim 7013, Norway.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Humans
Nanopore Sequencing*
Nanopores*
Nucleotides
Sequence Analysis, DNA
Software

Substances

Nucleotides