# Methylmap: visualization of modified nucleotides for large cohort sizes

## TL;DR

Methylmap is a tool for visualizing DNA methylation patterns in large groups of people, helping researchers study epigenetics more effectively.

## Contribution

Methylmap introduces a new visualization tool optimized for large cohorts and provides haplotype-specific methylation data from 226 individuals.

## Key findings

- Methylmap is optimized for visualizing nucleotide modifications in large cohorts.
- The tool includes haplotype-specific methylation data from 226 individuals sequenced using Oxford Nanopore Technologies.
- Methylmap is available as a web application and command-line tool for broad accessibility.

## Abstract

Over the years, there has been growing interest in epigenetics, where nucleotide modifications are increasingly recognized for their roles in health and disease. Understanding methylation patterns at the nucleotide level has become pivotal for advancing this field. However, visualizing these modifications, particularly in cohorts of more than a few individuals, remains a challenge.

Here, we present methylmap, a tool developed to visualize modified nucleotide frequencies for regions of interest, specifically optimized for cohort sizes with more than a few individuals. Furthermore, methylmap features the visualization of the haplotype-specific methylation status of 226 individuals of the 1000 Genomes Project ONT Sequencing Consortium, sequenced using the Oxford Nanopore Technologies PromethION. This resource provides the research community with a comprehensive and complete overview of genome-wide methylation patterns.

Methylmap offers an easy-to-use platform to facilitate epigenetic research. It is available both as a web application at https://methylmap.bioinf.be and as a command-line tool through Bioconda and PyPI. As such, we provide a valuable resource for advancing the understanding of epigenetic modifications in health and disease.

The online version contains supplementary material available at 10.1186/s12859-025-06106-3.