Novel Computational Pipeline for Comparative Whole-Genome Methylation Profiling In Bacteria

Novel Computational Pipeline for Comparative Whole-Genome Methylation Profiling In Bacteria

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DNA methylation is an important epigenetic mechanism in bacteria, involved in processes such as gene regulation, virulence, and antimicrobial resistance. Despite advances in long-read sequencing technologies, comparing methylation patterns across multiple bacterial strains remains challenging, largely due to genomic variability and the lack of standardized analytical approaches. In this study, we present a novel pipeline for the analysis of DNA methylation in Klebsiella pneumoniae using data from nanopore sequencing. The workflow supports two alignment strategies: mapping to a universal reference genome or to a sample-specific reference constructed de novo. This flexible approach enables both broad inter-strain comparisons and detailed strain-specific analyses, facilitating consistent and interpretable investigation of methylation patterns across diverse bacterial genomes.

DNA methylation is an important epigenetic mechanism in bacteria, involved in processes such as gene regulation, virulence, and antimicrobial resistance. Despite advances in long-read sequencing technologies, comparing methylation patterns across multiple bacterial strains remains challenging, largely due to genomic variability and the lack of standardized analytical approaches. In this study, we present a novel pipeline for the analysis of DNA methylation in Klebsiella pneumoniae using data from nanopore sequencing. The workflow supports two alignment strategies: mapping to a universal reference genome or to a sample-specific reference constructed de novo. This flexible approach enables both broad inter-strain comparisons and detailed strain-specific analyses, facilitating consistent and interpretable investigation of methylation patterns across diverse bacterial genomes.

nanopore sequencing; DNA methylation; whole genome sequencing; alignment; Klebsiella pneumoniae

nanopore sequencing; DNA methylation; whole genome sequencing; alignment; Klebsiella pneumoniae

ZBUDILOVÁ, M.; JAKUBÍČKOVÁ, M.; VÍTKOVÁ, H.

17.08.2025

Avestia Publishing

978-1-990800-61-0

Proceedings of the World Congress on Electrical Engineering and Computer Systems and Science

7

https://international-aset.net/avestia.com/EECSS2025_Proceedings/files/paper/ICBES/ICBES_156.pdf