cfDNApipe：一种用于游离 DNA 高通量测序数据的全面质量控制和分析流程。

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

机构信息

Ministry 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.

Department of Physics, Tsinghua University, Beijing 100084, China.

出版信息

Bioinformatics. 2021 Nov 18;37(22):4251-4252. doi: 10.1093/bioinformatics/btab413.

DOI:10.1093/bioinformatics/btab413

PMID:34042972

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9502158/

Abstract

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.

摘要

动机

无细胞 DNA（cfDNA）作为液体活检的一种有前途的标志物，正受到生物和临床领域的广泛关注。cfDNA 高通量测序（HTS）数据已经发现了许多与疾病相关的特征。然而，cfDNA HTS 数据分析和质量控制（QC）仍然缺乏综合和系统的工具。

结果

在这里，我们提出了 cfDNApipe，这是一个易于使用的、用于 cfDNA 全基因组测序（WGS）和全基因组亚硫酸氢盐测序（WGBS）数据分析的系统 python 包。它涵盖了 cfDNA 数据的整个分析流程，包括原始测序数据处理、QC 和复杂的统计分析，如检测拷贝数变异（CNVs）、差异甲基化区域和 DNA 片段大小改变。cfDNApipe 提供了一键式执行的流水线和灵活的应用程序编程接口，用于定制分析。