cfDNApipe

cfDNApipe is a comprehensive Python package for analyzing cell-free DNA (cfDNA) whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) data. It addresses the growing interest in cfDNA as a biomarker for liquid biopsies in biological and clinical research. Despite the discovery of disease-related features from cfDNA high-throughput sequencing (HTS) data, there has been a notable absence of integrative tools for systematic data analysis and quality control (QC).

cfDNApipe fills this gap by offering an easy-to-use solution that spans the entire analysis workflow for cfDNA data, including processing raw sequencing data, conducting quality control, and performing advanced statistical analyses. These analyses encompass detecting copy number variations (CNVs), identifying differentially methylated regions, and analyzing DNA fragment size alterations. cfDNApipe supports one-command-line execution for standard analyses and provides flexible application programming interfaces for tailored analysis needs.