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High-throughput sequencing (HTS) methods for eccDNA identification are continually evolving. However, an efficient pipeline for the integrative and comprehensive analysis of eccDNA obtained from HTS data is still lacking. Here, we introduce eccDNA-pipe, an accessible software package that offers a user-friendly pipeline for conducting eccDNA analysis starting from raw sequencing data. This dataset includes data from various sequencing techniques such as whole-genome sequencing (WGS), Circle-seq and Circulome-seq, obtained through short-read sequencing or long-read sequencing. eccDNA-pipe presents a comprehensive solution for both upstream and downstream analysis, encompassing quality control and eccDNA identification in upstream analysis and downstream tasks such as eccDNA length distribution analysis, differential analysis of genes enriched with eccDNA and visualization of eccDNA structures. Notably, eccDNA-pipe automatically generates high-quality publication-ready plots. In summary, eccDNA-pipe provides a comprehensive and user-friendly pipeline for \ufeffcustomized analysis of eccDNA research.<\/jats:p>","DOI":"10.1093\/bib\/bbae034","type":"journal-article","created":{"date-parts":[[2024,2,13]],"date-time":"2024-02-13T11:47:00Z","timestamp":1707824820000},"source":"Crossref","is-referenced-by-count":13,"title":["eccDNA-pipe: an integrated pipeline for identification, analysis and visualization of extrachromosomal circular DNA from high-throughput sequencing data"],"prefix":"10.1093","volume":"25","author":[{"given":"Minghao","family":"Fang","sequence":"first","affiliation":[{"name":"Department of Oncology , The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, , Hefei, 230027 , China"},{"name":"University of Science and Technology of China , The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, , Hefei, 230027 , China"},{"name":"Institute of Advanced Technology, University of Science and Technology of China , Hefei, 230027 , China"},{"name":"Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence , Hefei Comprehensive National Science Center, Hefei, 230088 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingwen","family":"Fang","sequence":"additional","affiliation":[{"name":"Department of Oncology , The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, , Hefei, 230027 , China"},{"name":"University of Science and Technology of China , The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, , Hefei, 230027 , China"},{"name":"HanGene Biotech, Xiaoshan Innovation Polis , Hangzhou, Zhejiang 311200 , China"},{"name":"Suzhou Institute for Advanced Research, University of Science and Technology of China 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