Journal
BIOINFORMATICS
Volume 37, Issue 22, Pages 4251-4252Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btab413
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Funding
- National Natural Science Foundation of China [61773230, 61721003]
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cfDNApipe is an easy-to-use and systematic python package for cfDNA whole-genome sequencing and whole-genome bisulfite sequencing data analysis, covering the entire analysis pipeline, quality control, and statistical analysis.
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.
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