MethylExtract

MethylExtract performs high-resolution whole-genome DNA methylation profiling and simultaneous detection of sequence variation from bisulfite-treated sequencing reads.

Key Features:

• High-Quality Methylation Mapping: Generates comprehensive whole genome methylation maps at single-cytosine resolution by aligning bisulfite-treated sequence reads to a reference genome and profiling methylation levels.
• Simultaneous Detection of Sequence Variation: Identifies single nucleotide variants and genotypes from the same bisulfite-treated data using a VarScan-like approach for sensitive SNV and genotype calling.
• Error Source Management: Accounts for sequencing errors, incomplete bisulfite conversion (bisulfite failure), clonal reads, and SNVs and includes a statistical assessment of bisulfite conversion efficiency.

Scientific Applications:

• Genetic–epigenetic interaction studies: Enables analysis of the interplay between genetic variants and differential DNA methylation by providing concurrent methylation and SNV calls.
• Cancer epigenetics: Supports profiling of tumor methylation patterns alongside somatic variant detection to study epigenetic alterations in cancer.
• Developmental biology: Facilitates investigation of DNA methylation dynamics during development.
• Complex trait analysis: Allows integrative analyses of methylation and genetic variation in studies of complex traits.

Methodology:

Aligns bisulfite-treated reads to a reference genome, profiles methylation levels at single cytosines, detects SNVs using VarScan-like algorithms, performs statistical assessment of bisulfite conversion efficiency, and has been benchmarked against artificial bisulfite-treated datasets and compared with Bis-SNP.