cfDNApipe: a comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data

Area of Science:

• Genomics and Bioinformatics
• Molecular Biology
• Clinical Diagnostics

Background:

• Cell-free DNA (cfDNA) is a valuable biomarker for liquid biopsy, offering insights into various diseases through high-throughput sequencing (HTS).
• Existing HTS data analysis tools for cfDNA lack integration and systematic quality control (QC).

Purpose of the Study:

• To develop and present cfDNApipe, a user-friendly Python package for comprehensive cfDNA HTS data analysis.
• To provide a systematic pipeline for cfDNA whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) data.

Main Methods:

• Development of a Python package, cfDNApipe, integrating raw data processing, QC, and advanced statistical analyses.
• Implementation of one-command-line pipelines and flexible APIs for cfDNA WGS and WGBS data.
• Analysis includes detection of copy number variations (CNVs), differentially methylated regions, and DNA fragment size alterations.

Main Results:

• cfDNApipe offers a systematic and integrated solution for cfDNA HTS data analysis.
• The package facilitates robust QC and sophisticated analyses, including CNV detection, methylation analysis, and fragment size profiling.
• Provides both automated pipelines and customizable options for diverse research needs.

Conclusions:

• cfDNApipe addresses the need for systematic tools in cfDNA HTS data analysis.
• The package enhances the utility of cfDNA as a biomarker in liquid biopsy by enabling comprehensive data interpretation.
• Facilitates advancements in biological and clinical applications of cfDNA research.