NANOME: A Nextflow pipeline for haplotype-aware allele-specific consensus DNA methylation detection by nanopore long-read sequencing.

ABSTRACT: Nanopore long-read sequencing has expanded the capacity of long-range, single-base, and single-molecule DNA-methylation (DNAme) detection and haplotype-aware allele-specific epigenetic phasing. Previously, we benchmarked and ranked the robustness of seven computational tools for DNAme detection using nanopore sequencing. The top performers were Megalodon, Nanopolish, DeepSignal and Guppy. However, these algorithms exhibit lower performance at regions with discordant non-singleton DNAme patterns compared to genome-wide regions. Furthermore, long-read sequencing analysis of mammalian genomes requires higher computational resources than next-generation sequencing. To address these issues, we developed a NANOpore Methylation (NANOME) a consensus DNAme predictive model using XGBoost, which inte

SUBMITTER: Liu Y 

PROVIDER: S-EPMC12236756 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature