Sherman

Sherman integrates outputs from multiple bisulfite-read mappers to improve detection of methylated cytosines in whole genome bisulfite sequencing (WGBS) data.

Key Features:

• Multi-mapper integration: Integrates mapping results from Bismark, BSMAP, and BS-seeker2 to leverage complementary mapper strengths.
• Scoring system: Applies a scoring system to combine mapper outputs and prioritize concordant mappings.
• Enhanced cytosine detection: Increases the number of detected cytosines compared with using Bismark alone.
• Robustness to artifacts: Improves robustness against bisulfite-induced DNA damage and sequencing artifacts.
• Stability across read conditions: Reduces fluctuations in detection accuracy caused by variable read conditions.
• Exploits complementarity: Leverages the mutual complementarity of mapping outcomes under various read conditions.
• Sample classification: Enables classification of WGBS samples by tissue origin using CpG and CpH methylation patterns.
• Public dataset analysis: Facilitates comprehensive analyses of public WGBS datasets.

Scientific Applications:

• Genome-wide methylation profiling: Detection and profiling of DNA methylation at single-nucleotide resolution from WGBS data.
• Improved methylation calling: More comprehensive identification of methylated cytosines across CpG and CpH contexts.
• Tissue-of-origin classification: Classification of samples according to tissue origin based on CpG and CpH methylation patterns.
• Analysis of heterogeneous reads: Stabilizing methylation detection in datasets with variable read quality or bisulfite-induced damage.

Methodology:

Integrates mapping outputs from Bismark, BSMAP, and BS-seeker2 and applies a scoring system to combine their complementary mapping results.