memod-s: a standardised workflow to explore and analyse prokaryotic methylation patterns for Nanopore sequencing data

Area of Science:

• Genomics
• Bioinformatics
• Epigenetics

Background:

• Bacterial epigenome understanding is crucial for gene regulation and host-pathogen interactions.
• Third-generation sequencing (e.g., Oxford Nanopore) allows direct DNA modification detection for epigenomic studies.
• Analyzing Nanopore data is complex, computationally intensive, and lacks integrated pipelines.

Purpose of the Study:

• To develop a comprehensive, user-friendly workflow for Nanopore-based bacterial epigenome analysis.
• To integrate multiple analysis steps, including basecalling, quality control, genome assembly, annotation, and methylation profiling.
• To provide automated genome-wide methylation profiling with integrated visualizations and statistics.

Main Methods:

• Developed memod-s, a Snakemake-based workflow.
• Integrated state-of-the-art tools for Nanopore data analysis.
• Designed a modular and user-friendly pipeline.

Main Results:

• memod-s simplifies the entire Nanopore data analysis process.
• The workflow produces comprehensive genome-wide methylation profiles with visualizations and statistics.
• It reduces complexity and provides insights into bacterial methylation patterns.

Conclusions:

• memod-s offers an efficient and accessible solution for bacterial epigenome analysis.
• The workflow facilitates deeper understanding of bacterial gene regulation and adaptation.
• memod-s is available as open source for the scientific community.