MethylCoder

MethylCoder processes bisulfite-treated sequencing reads to generate per-base DNA methylation calls for epigenetic analyses.

Key Features:

• Per-Base Methylation Data Generation: Produces precise per-base methylation information from bisulfite-treated reads.
• Alignment Flexibility: Supports two distinct short-read aligners for mapping bisulfite-converted reads.
• Handling Complex Alignments: Manages soft-masked alignments and overlapping paired-end reads to improve mapping accuracy.
• Output Formats: Exports methylation results in text and binary formats and writes final alignments in SAM format.
• Methylation Context and Levels: Determines methylation context (CG/CHG/CHH) and reports methylation levels.
• Coverage and C-T Conversion Reporting: Provides comprehensive coverage data and C-T conversion information essential for bisulfite analysis.
• Performance Efficiency: Optimized for competitive speed and memory usage for large-scale methylation analyses.

Scientific Applications:

• Epigenetic profiling: Generates detailed methylation maps to support studies of epigenetic variation and patterns.
• Gene regulation analysis: Enables investigation of DNA methylation roles in gene regulation mechanisms.
• Disease-associated methylation studies: Supports analysis of aberrant methylation in disease contexts such as cancer.

Methodology:

Processes bisulfite-treated reads through alignment using selected short-read aligners, handles soft-masked and overlapping paired-end alignments, and analyzes C-T conversions to determine methylation context (CG/CHG/CHH), methylation levels, and coverage; outputs include text/binary methylation files and SAM alignments.