cfDNApipe

cfDNApipe analyzes cell-free DNA high-throughput sequencing data from whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) to detect genomic and epigenetic alterations associated with disease.

Key Features:

• Integrated cfDNA Analysis Pipeline: Processes raw cfDNA high-throughput sequencing data from WGS and WGBS experiments within a unified computational workflow.
• Quality Control Analysis: Performs systematic quality control procedures to assess sequencing data quality in cfDNA datasets.
• Copy Number Variation Detection: Identifies copy number variations from cfDNA sequencing data.
• DNA Methylation Analysis: Detects differentially methylated regions from whole-genome bisulfite sequencing data.
• Fragment Size Analysis: Analyzes cfDNA fragment length distributions to identify disease-associated fragmentation patterns.

Scientific Applications:

• Liquid Biopsy Analysis: Investigates genomic and epigenetic biomarkers in circulating cell-free DNA for disease detection.
• Cancer Genomics: Identifies tumor-associated copy number alterations and methylation changes from cfDNA sequencing data.
• Clinical Genomics Research: Supports analysis of cfDNA features for applications including oncology, prenatal testing, and transplant monitoring.

Methodology:

cfDNApipe processes whole-genome sequencing and whole-genome bisulfite sequencing data from cell-free DNA and performs quality control, copy number variation detection, differential methylation analysis, and fragment size distribution analysis.