Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase

Area of Science:

• Genomics
• Bioinformatics
• Epigenetics

Background:

• Nanopore sequencing offers long reads and modified nucleotide detection, ideal for allele-specific methylation analysis.
• Existing software lacks comprehensive tools for SNP detection, haplotype phasing, and methylation mapping from nanopore data.

Purpose of the Study:

• To develop and present NanoMethPhase and SNVoter, integrated software for analyzing allele-specific methylation from nanopore sequencing data.
• To enable accurate genome-wide detection and phasing of 5-methylcytosine with improved single nucleotide variant calling.

Main Methods:

• Development of NanoMethPhase for phasing 5-methylcytosine in nanopore sequencing data.
• Implementation of SNVoter for post-processing nanopore single nucleotide variant calls to enhance accuracy.
• Integration of both tools for comprehensive allele-specific methylation analysis.

Main Results:

• NanoMethPhase accurately phases 5-methylcytosine from nanopore sequencing data.
• SNVoter improves the accuracy of single nucleotide variant calls, particularly in low-coverage areas.
• The combined tools achieve accurate genome-wide allele-specific methylation detection with approximately tenfold redundancy.

Conclusions:

• NanoMethPhase and SNVoter provide a complete software solution for allele-specific methylation analysis using nanopore sequencing.
• These tools facilitate accurate genome-wide methylation phasing and SNP detection, even with limited sequencing depth.
• The developed software advances the utility of nanopore sequencing for epigenetic studies.