cfdnakit

cfdnakit analyzes shallow whole-genome sequencing (~0.3X or more) of cell-free DNA (cfDNA) by extracting cfDNA fragment lengths and calculating ctDNA estimation scores (CES).

Key Features:

• Fragment Length Extraction: Extracts the length of cfDNA fragments from sequencing data.
• Fragment-Length Visualization: Aids visualization of fragment-length information.
• Bin-Based Fragment Analysis: Extracts fragment-length information per non-overlapping fixed-sized bins.
• ctDNA Estimation Score (CES): Calculates CES using bin-based fragment-length information.

Scientific Applications:

• Cell-free DNA Analysis: Supports analysis of shallow whole-genome sequencing of cfDNA for liquid biopsy applications.
• Circulating Tumor DNA Monitoring: Enables ctDNA estimation through fragment-length profiling.

Methodology:

The package processes shallow whole-genome sequencing data (~0.3X or more) to extract cfDNA fragment lengths, aggregates fragment-length information across non-overlapping fixed-sized bins, and computes ctDNA estimation scores (CES) from these binned fragment-length profiles.