pycoMeth

pycoMeth stores and analyzes DNA methylation calls from Oxford Nanopore Technologies (ONT) long-read sequencing to perform haplotype-aware, multi-sample differential methylation analysis.

Key Features:

• MetH5 storage format: MetH5 is a read-level, reference-anchored format for ONT methylation calls optimized for rapid access and large-scale data management.
• Haplotype-aware, multi-sample consensus segmentation: Implements haplotype-aware, multi-sample consensus segmentation algorithms to define segments across samples.
• Differential methylation testing: Performs differential methylation testing to detect differentially methylated regions (DMRs) across samples.
• Performance and sensitivity: Segmentation and differential methylation testing exhibit increased performance and sensitivity compared to tools designed for short-read methylation data.
• Benchmarking: Benchmarking studies show MetH5 outperforms existing solutions in efficiency for storing ONT methylation calls.

Scientific Applications:

• Differential methylation studies: Enables comprehensive analysis of differential methylation across biological samples using ONT long-read data.
• Haplotype-specific methylation: Supports exploration of haplotype-specific methylation patterns and allele-specific epigenetic analyses.
• Complex genomic region analysis: Improves accuracy and reliability of methylation analysis in complex genomic regions by leveraging long reads.

Methodology:

Uses the MetH5 read-level, reference-anchored storage format combined with haplotype-aware, multi-sample consensus segmentation algorithms followed by differential methylation testing.