Related Experiment Video
Updated: Nov 4, 2025
Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
Published on: June 8, 2020
cfDNApipe: a comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data
Wei Zhang1, Lei Wei1, Jiaqi Huang2
1Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China.
Motivation:
Cell-free DNA (cfDNA) is gaining substantial attention from both biological and clinical fields as a promising marker for liquid biopsy. Many aspects of disease-related features have been discovered from cfDNA high-throughput sequencing (HTS) data. However, there is still a lack of integrative and systematic tools for cfDNA HTS data analysis and quality control (QC).
Results:
Here, we propose cfDNApipe, an easy-to-use and systematic python package for cfDNA whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) data analysis. It covers the entire analysis pipeline for the cfDNA data, including raw sequencing data processing, QC and sophisticated statistical analysis such as detecting copy number variations (CNVs), differentially methylated regions and DNA fragment size alterations. cfDNApipe provides one-command-line-execution pipelines and flexible application programming interfaces for customized analysis.
Availability And Implementation:
https://xwanglabthu.github.io/cfDNApipe/.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
More Related Videos
13:24Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
Published on: April 11, 2016
09:06High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq
Published on: October 5, 2018
