Methpipe

Methpipe analyzes bisulfite sequencing data (WGBS and RRBS) to estimate DNA methylation at single-base resolution for the study of methylome patterns.

Key Features:

• Mapping and methylation estimation: Maps bisulfite sequencing reads to reference genomes and estimates methylation levels at individual cytosine sites.
• Identification of methylome features: Detects hypo-methylated regions (HMR), partially methylated domains (PMD), hyper-methylated regions (HyperMR), and allele-specific methylated regions (AMR).
• Comparative methylome analysis: Performs comparative analyses of methylomes across samples and public whole-genome bisulfite sequencing datasets.
• Integration with MethBase: Integrates with MethBase, an annotated database of public-domain methylomes, to extract and compare methylome features.

Scientific Applications:

• Gene regulation: Resolves single-base and regional methylation patterns to investigate DNA methylation roles in gene regulation.
• Evolutionary biology: Enables comparative methylome analyses for evolutionary and comparative genomics studies.
• Disease research: Facilitates investigation of methylation changes associated with disease mechanisms and pathology.
• Allele-specific methylation studies: Identifies AMRs to study imprinting and allele-specific regulatory phenomena.

Methodology:

Performs bisulfite read mapping to reference genomes, estimates methylation levels at cytosines, detects HMR/PMD/HyperMR/AMR, and conducts comparative analyses using MethBase.