methylGrapher

methylGrapher maps whole genome bisulfite sequencing data to genome graphs for accurate DNA methylation analysis and reconstruction of methylation patterns along haplotype paths.

Key Features:

• Genome graph mapping: Maps WGBS data to genome graphs including the draft human pangenome graph rather than linear reference genomes.
• Haplotype-resolved methylation reconstruction: Reconstructs methylation patterns along haplotype paths precisely and efficiently.
• Increased CpG detection: Captures a substantial number of CpG sites that are missed by linear reference-based methods.
• Reduced reference bias: Improves overall genome coverage while reducing alignment reference bias compared to linear genome analysis approaches.
• Benchmarking compatibility: Fully recapitulates DNA methylation patterns defined by classic linear genome analysis approaches for validation.

Scientific Applications:

• Human Pangenome methylation analysis: Enables DNA methylation analysis using the draft human pangenome graph to transcend the limits of traditional linear reference genomes.
• Population-scale WGBS studies: Processes WGBS data from diverse individuals whose genomes are represented in pangenome graphs, as demonstrated with five individuals from the first Human Pangenome draft and ENCODE EN-TEx data.
• Epigenetic variant detection: Identifies methylation patterns at genetic loci that may be inaccessible or misaligned in linear reference-based approaches due to genetic diversity.

Methodology:

methylGrapher maps WGBS reads to a genome graph and reconstructs methylation patterns along haplotype paths.