cvlr

cvlr identifies heterogeneously methylated genomic regions from Oxford Nanopore Technologies (ONT) long reads by extracting CpG methylation patterns and characterizing subpopulation-specific epigenetic states.

Key Features:

• Long-Read Methylation Analysis: Leverages ONT long-read sequencing to examine CpG methylation patterns across extended genomic regions.
• Subpopulation Identification: Uses a clustering algorithm to define subpopulations of molecules based on distinct methylation patterns.
• Heterogeneous Methylation Detection: Scans genomic windows (e.g., on chromosome 15) to identify regions exhibiting heterogeneous methylation.
• Covariance Computation: Computes covariance of methylation across identified regions while accounting for mixtures of different read types.

Scientific Applications:

• Epigenetic Research: Characterizes heterogeneous CpG methylation landscapes to inform studies of epigenetic regulation.
• Disease Studies: Detects variable methylation patterns relevant to investigations of aberrant methylation in disease.
• Genomic Imprinting Analysis: Identifies heterogeneous methylation at known imprinted loci to study parent-of-origin effects.

Methodology:

Processes ONT reads to extract methylation information at CpG sites, applies a clustering algorithm to identify methylation-based subpopulations, scans genomic windows (e.g., chromosome 15) to detect heterogeneous methylation, and computes covariance of methylation across identified regions accounting for read-type mixtures.