Exploring Microbial Methylation With Nanopore Epigenomics and Analysis

Hidden in Plain Sight: Exploring Bacterial Methylation with Nanopore Epigenomic Sequencing DNA methylation is a key component of bacterial genome biology, influencing gene regulation, restriction-modification systems, and adaptation. The ability to detect these modifications directly with nanopore sequencing has accelerated research, but it also requires reliable references and curated datasets to ensure accuracy. In this webinar, we introduce the ATCC Genome Portal (AGP) — the only authenticated reference genome database for ATCC microbial strains and cell lines. We’ll explore how the AGP delivers high-quality assemblies, annotations, and methylation data, and demonstrate its value for applications such as comparative methylation analysis, epigenomic diversity studies, and genome defense mechanism research. Using Helicobacter pylori as a case study, we will highlight practical approaches for moving from assemblies and BED files to comparative motif analysis. Finally, we’ll cover Oxford Nanopore best practices for basecalling, assembly, and polishing, including QC considerations and common pitfalls. We’ll also demonstrate how to extract and analyse modification data and perform motif analysis with the Modkit tool. Bioinformatics specialist will also share insights into when and where to use the new v6 HAC (High Accuracy) or SUP (Super Accuracy) models in bacterial workflows.