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Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells
Published on: April 4, 2016
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eccDNA-pipe: an integrated pipeline for identification, analysis and visualization of extrachromosomal circular DNA
Minghao Fang1,2,3, Jingwen Fang1,4,5, Songwen Luo1
1Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
Briefings in Bioinformatics
|February 13, 2024
Summary
A new software package, eccDNA-pipe, offers a user-friendly pipeline for analyzing extrachromosomal circular DNA (eccDNA) from high-throughput sequencing data. This tool facilitates comprehensive eccDNA research from raw data to publication-ready visualizations.
Area of Science:
- Genomics
- Bioinformatics
- Cancer Research
Background:
- Extrachromosomal circular DNA (eccDNA) plays a crucial role in tumor development.
- High-throughput sequencing (HTS) methods for eccDNA detection are advancing.
- A lack of integrated pipelines hinders comprehensive eccDNA analysis from HTS data.
Purpose of the Study:
- To introduce eccDNA-pipe, a user-friendly software package for eccDNA analysis.
- To provide a comprehensive pipeline for analyzing eccDNA from raw sequencing data.
- To support various sequencing techniques including WGS, Circle-seq, and Circulome-seq.
Main Methods:
- Developed eccDNA-pipe, an accessible software package.
- Integrated upstream analysis: quality control and eccDNA identification.
- Incorporated downstream analysis: length distribution, differential gene enrichment, and structural visualization.
Main Results:
- eccDNA-pipe handles data from short-read and long-read sequencing.
- The pipeline automates quality control and eccDNA identification.
- Publication-ready plots are automatically generated for enhanced data presentation.
Conclusions:
- eccDNA-pipe offers a comprehensive and user-friendly solution for eccDNA research.
- The software facilitates customized analysis of eccDNA from HTS data.
- This tool addresses the need for an efficient eccDNA analysis pipeline.
