BatMeth2

BatMeth2 performs indel-sensitive alignment and methylation calling of bisulfite sequencing (BS-Seq) reads to generate single-base-resolution DNA methylation profiles across genomes.

Key Features:

• Indel-Sensitive Mapping: An advanced algorithm aligns bisulfite-treated reads with high precision in the presence of variable-length insertions and deletions relative to a reference genome.
• Comprehensive Methylation Analysis: Calculates methylation levels at individual cytosines and across broader genomic or functional regions, including genes and transposable elements.
• Integrated Annotation and Visualization: Includes programs that provide detailed annotation of methylation data and enable visualization of methylation patterns.
• DMC/DMR Identification: Supports identification of differentially methylated cytosines and regions (DMCs/DMRs) for downstream epigenetic analysis.

Scientific Applications:

• Epigenomic profiling in eukaryotes: Enables single-base-resolution studies of DNA methylation to investigate functional regulatory mechanisms in eukaryotic organisms.
• Study of genomic variation effects: Improves methylation calling accuracy in regions adjacent to indels, supporting analyses of how genomic variation impacts epigenetic state.
• Development and disease research: Facilitates detection and characterization of methylation changes associated with development and disease processes.

Methodology:

Indel-sensitive alignment of bisulfite-treated reads; computation of methylation levels at single loci and across genes and transposable elements; integrated annotation and visualization modules; validation using simulated and real datasets.