wg-blimp

wg-blimp analyzes whole-genome bisulfite sequencing (WGBS) data to call methylated cytosines, detect differentially methylated regions (DMRs), and segment the methylome for epigenetic studies.

Key Features:

• End-to-End Pipeline: Performs a complete WGBS analysis workflow starting from raw sequencing data and a reference genome.
• Alignment: Aligns bisulfite-treated reads to a reference genome for downstream methylation analysis.
• Quality Control (QC): Executes QC steps to assess and ensure data quality during processing.
• Methylation Calling: Calls methylated cytosines across the genome from aligned bisulfite reads.
• Detection of Differentially Methylated Regions (DMRs): Identifies genomic regions with significant methylation differences between conditions or samples.
• Methylome Segmentation: Segments the genome into regions based on methylation patterning.
• Comprehensive Analysis Workflow: Integrates alignment, QC, methylation calling, DMR detection, and segmentation to produce consistent analytical outputs.

Scientific Applications:

• Epigenetic research: Enables genome-wide characterization of DNA methylation patterns from WGBS data.
• Gene regulation studies: Supports identification of methylation changes relevant to transcriptional regulation via DMR detection.
• Developmental biology: Facilitates analysis of methylation dynamics during development, including embryonic stem cells.
• Disease mechanism investigation: Assists in detecting epigenetic alterations associated with disease mechanisms.
• Cross-platform robustness assessment: Applicable to comparisons across different reference genomes and sequencing techniques.

Methodology:

Requires raw sequencing data and a reference genome and sequentially performs alignment of bisulfite-treated reads, quality control, methylation calling, DMR detection, and methylome segmentation.