SAAP-BS

SAAP-BS performs comprehensive analysis and annotation of reduced representation bisulfite sequencing (RRBS) data to generate annotated CpG methylation reports for genome-wide methylation profiling.

Key Features:

• RRBS-specific processing: Implements processing steps tailored to reduced representation bisulfite sequencing data to profile CpG methylation.
• Read quality assessment and cleanup: Performs read quality evaluation and preprocessing to remove low-quality sequence data.
• Read alignment: Aligns sequencing reads to a reference genome for methylation calling.
• Methylation extraction: Extracts methylation information from aligned bisulfite sequencing reads to produce CpG-level methylation calls.
• Annotation: Annotates CpG methylation calls with genomic features.
• Reporting: Generates annotated CpG methylation reports summarizing methylation metrics.
• Visualization: Produces visual outputs for interpretation of methylation patterns.

Scientific Applications:

• Genome-wide methylation profiling: Generation of CpG methylation maps from RRBS datasets.
• Epigenetic modification studies: Analysis of DNA methylation changes associated with regulatory and epigenetic processes.
• Cancer biology: Investigation of methylation alterations relevant to tumorigenesis and cancer biomarkers.
• Developmental biology: Study of methylation dynamics during development and differentiation.
• Genetic disorder research: Examination of methylation patterns linked to inherited or acquired genetic disorders.

Methodology:

Performs read quality assessment and cleanup, aligns RRBS reads to a reference genome, extracts CpG methylation calls from bisulfite sequencing data, annotates methylation calls with genomic features, and generates reports and visualizations.