Methylator: A Modular Framework for DNA Methylation Analysis in Mammals and Plants Using Galaxy

TL;DR

Methylator is a user-friendly, modular framework integrated into Galaxy that enables comprehensive, cross-species DNA methylation analysis for mammals and plants, supporting diverse protocols and providing interactive visualizations.

Contribution

It introduces Methylator, a novel, accessible, end-to-end DNA methylation analysis framework with unique features like the Dirty-Harry alignment method and Galaxy integration.

Findings

Supports multiple methylation protocols (WGBS, RRBS, PBAT)

Handles all methylation contexts (CpG, CHG, CHH)

Provides interactive visualizations and reproducible workflows

Abstract

DNA cytosine methylation is a critical epigenetic mark regulating gene expression and thus playing an important role in development and differentiation across eukaryotes. Existing tools for high-throughput methylation analysis often lack cross-species flexibility or require command-line expertise. We present Methylator, a novel, end-to-end DNA methylation analysis framework integrated into the Galaxy platform, enabling accessible DNA methylation analysis for mammals and plants. Methylator supports analyses from data obtained using diverse protocols like WGBS, RRBS, and PBAT and handles all contexts of DNA methylation (CpG, CHG, and CHH). The Methylator framework includes quality control, alignment, methylation calling, differential analysis, and functional analysis through reproducible, user-friendly workflows. Its unique Dirty-Harry alignment method enhances mapping efficiency, while a Shiny-based interface allows for interactive, publication-ready visualizations. Methylator is freely available, offering researchers a versatile, user-friendly solution for epigenomic studies.