mHapTools

mHapTools converts bisulfite sequencing (BS-seq) reads into a compact mHap format for storage and analysis of DNA methylation haplotypes (mHaps).

Key Features:

• mHap format: Encodes read-level CpG methylation and reduces BAM file size by 40- to 140-fold while preserving all read-level methylation information.
• Tabix compatibility: Produces Tabix-compatible indexing to enable fast random and region-specific access to mHap files.
• BAM/SAM conversion: Provides a command-line utility to convert BAM/SAM files from various platforms into the mHap format.
• Post-processing: Includes functionality for post-processing tasks specific to DNA methylation data stored in mHap format.
• RRBS database generation: Has been applied to process all publicly available human reduced representation bisulfite sequencing (RRBS) data into an extensive mHap database.

Scientific Applications:

• Methylation haplotype analysis: Enables analysis of DNA methylation haplotypes across individual reads rather than relying on mean CpG methylation.
• Efficient storage of BS-seq datasets: Compresses and stores large-scale bisulfite sequencing read-level methylation information for downstream analysis.
• Region-specific querying: Supports rapid retrieval of methylation data for specific genomic regions via Tabix-indexed mHap files.
• Large-scale RRBS studies and comparative epigenomics: Facilitates population-scale analyses using the comprehensive human RRBS mHap database.

Methodology:

Converts BAM/SAM BS-seq reads into the mHap format, compresses read-level CpG methylation representation (40- to 140-fold BAM size reduction), produces Tabix-compatible indexing for random access, and supports post-processing of mHap files; applied to process public human RRBS data into an mHap database.