cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data
| Autor: | Jiaqi Li, Juhong Liu, Hairong Lv, Hanwen Xu, Jia-Qi Huang, Xiaowo Wang, Shuying He, Bixi Zhong, Yu Liu, Lei Wei, Wei Zhang |
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| Rok vydání: | 2021 |
| Předmět: |
Statistics and Probability
0303 health sciences Computer science Bisulfite sequencing Computational biology Python (programming language) Biochemistry Pipeline (software) DNA sequencing Computer Science Applications 03 medical and health sciences Computational Mathematics 0302 clinical medicine Differentially methylated regions Computational Theory and Mathematics Cell-free fetal DNA 030220 oncology & carcinogenesis Copy-number variation Liquid biopsy Molecular Biology computer 030304 developmental biology computer.programming_language |
| Zdroj: | Bioinformatics (Oxford, England). |
| ISSN: | 1367-4811 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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