iMeta (Feb 2025)
EasyMetagenome: A user‐friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research
- Defeng Bai,
- Tong Chen,
- Jiani Xun,
- Chuang Ma,
- Hao Luo,
- Haifei Yang,
- Chen Cao,
- Xiaofeng Cao,
- Jianzhou Cui,
- Yuan‐Ping Deng,
- Zhaochao Deng,
- Wenxin Dong,
- Wenxue Dong,
- Juan Du,
- Qunkai Fang,
- Wei Fang,
- Yue Fang,
- Fangtian Fu,
- Min Fu,
- Yi‐Tian Fu,
- He Gao,
- Jingping Ge,
- Qinglong Gong,
- Lunda Gu,
- Peng Guo,
- Yuhao Guo,
- Tang Hai,
- Hao Liu,
- Jieqiang He,
- Zi‐Yang He,
- Huiyu Hou,
- Can Huang,
- Shuai Ji,
- ChangHai Jiang,
- Gui‐Lai Jiang,
- Lingjuan Jiang,
- Ling N. Jin,
- Yuhe Kan,
- Da Kang,
- Jin Kou,
- Ka‐Lung Lam,
- Changchao Li,
- Chong Li,
- Fuyi Li,
- Liwei Li,
- Miao Li,
- Xin Li,
- Ye Li,
- Zheng‐Tao Li,
- Jing Liang,
- Yongxin Lin,
- Changzhen Liu,
- Danni Liu,
- Fengqin Liu,
- Jia Liu,
- Tianrui Liu,
- Tingting Liu,
- Xinyuan Liu,
- Yaqun Liu,
- Bangyan Liu,
- Minghao Liu,
- Wenbo Lou,
- Yaning Luan,
- Yuanyuan Luo,
- Hujie Lv,
- Tengfei Ma,
- Zongjiong Mai,
- Jiayuan Mo,
- Dongze Niu,
- Zhuo Pan,
- Heyuan Qi,
- Zhanyao Shi,
- Chunjiao Song,
- Fuxiang Sun,
- Yan Sun,
- Sihui Tian,
- Xiulin Wan,
- Guoliang Wang,
- Hongyang Wang,
- Hongyu Wang,
- Huanhuan Wang,
- Jing Wang,
- Jun Wang,
- Kang Wang,
- Leli Wang,
- Shao‐kun Wang,
- Xinlong Wang,
- Yao Wang,
- Zufei Xiao,
- Huichun Xing,
- Yifan Xu,
- Shu‐yan Yan,
- Li Yang,
- Song Yang,
- Yuanming Yang,
- Xiaofang Yao,
- Salsabeel Yousuf,
- Hao Yu,
- Yu Lei,
- Zhengrong Yuan,
- Meiyin Zeng,
- Chunfang Zhang,
- Chunge Zhang,
- Huimin Zhang,
- Jing Zhang,
- Na Zhang,
- Tianyuan Zhang,
- Yi‐Bo Zhang,
- Yupeng Zhang,
- Zheng Zhang,
- Mingda Zhou,
- Yuanping Zhou,
- Chengshuai Zhu,
- Lin Zhu,
- Yue Zhu,
- Zhihao Zhu,
- Hongqin Zou,
- Anna Zuo,
- Wenxuan Dong,
- Tao Wen,
- Shifu Chen,
- Guoliang Li,
- Yunyun Gao,
- Yong‐Xin Liu
Affiliations
- Defeng Bai
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China
- Tong Chen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao‐di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing China
- Jiani Xun
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China
- Chuang Ma
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China
- Hao Luo
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China
- Haifei Yang
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China
- Chen Cao
- Key Laboratory for Bio‐Electromagnetic Environment and Advanced Medical Theranostics, School of Biomedical Engineering and Informatics Nanjing Medical University Nanjing Jiangsu China
- Xiaofeng Cao
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment Tsinghua University Beijing China
- Jianzhou Cui
- Immunology Translational Research Programme, Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore
- Yuan‐Ping Deng
- Research Center for Parasites and Vectors, College of Veterinary Medicine Hunan Agricultural University Changsha Hunan China
- Zhaochao Deng
- Institute of Marine Biology and Pharmacology, Ocean College Zhejiang University Zhoushan Zhejiang China
- Wenxin Dong
- Agro‐Environmental Protection Institute Ministry of Agriculture and Rural Affairs Tianjin China
- Wenxue Dong
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine Xizang Minzu University Xianyang China
- Juan Du
- Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology Stockholm Sweden
- Qunkai Fang
- College of Environment Zhejiang University of Technology Hangzhou China
- Wei Fang
- College of Environmental and Resource Sciences Zhejiang Agriculture and Forestry University Hangzhou China
- Yue Fang
- The College of Forestry Beijing Forestry University Beijing China
- Fangtian Fu
- Department of Bioinformatics, Hangzhou VicrobX Biotech Co., Ltd Hangzhou Zhejiang China
- Min Fu
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, College of Plant Protection Anhui Agricultural University Hefei China
- Yi‐Tian Fu
- Xiangya School of Basic Medicine Central South University Changsha Hunan China
- He Gao
- Institute of Microbiology,Guangdong Academy of Sciences Guangzhou Guangdong China
- Jingping Ge
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, School of Life Sciences Heilongjiang University Harbin China
- Qinglong Gong
- College of Animal Science and Technology Jilin Agricultural University Changchun Jilin China
- Lunda Gu
- Sansure Biotech Incorporation Changsha Hunan China
- Peng Guo
- School of Food Science and Biology Hebei University of Science and Technology Shijiazhuang Hebei China
- Yuhao Guo
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, School of Life Sciences Heilongjiang University Harbin China
- Tang Hai
- School of Life Sciences Shanxi Datong University Datong China
- Hao Liu
- Department of Health & Environmental Sciences Xi'an Jiaotong‐Liverpool University Suzhou Jiangsu China
- Jieqiang He
- College of Horticulture Northwest A&F University Yangling Shaanxi China
- Zi‐Yang He
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science The University of Melbourne VIC Australia
- Huiyu Hou
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China
- Can Huang
- Graduate School of Frontier Sciences The University of Tokyo Kashiwa‐shi, Chiba Japan
- Shuai Ji
- Institute of Biotechnology, Helsinki Institute of Life Science University of Helsinki Helsinki Finland
- ChangHai Jiang
- Shanghai Maritime University Shanghai China
- Gui‐Lai Jiang
- Suzhou Medical College Soochow University Suzhou Jiangsu China
- Lingjuan Jiang
- Biomarker Discovery and Validation Facility, Institute of Clinical Medicine, Peking Union Medical College Hospital Beijing China
- Ling N. Jin
- Department of Civil and Environmental Engineering The Hong Kong Polytechnic University Hong Kong China
- Yuhe Kan
- College of Biology and Oceanography Weifang University Weifang Shandong China
- Da Kang
- College of Environmental Science and Engineering Beijing University of Technology Beijing China
- Jin Kou
- College of Environmental and Municipal Engineering Lanzhou Jiaotong University Lanzhou China
- Ka‐Lung Lam
- School of Life Sciences The Chinese University of Hong Kong Shatin, Hong Kong China
- Changchao Li
- Department of Civil and Environmental Engineering The Hong Kong Polytechnic University Hong Kong China
- Chong Li
- Department of Renewable Resources University of Alberta Edmonton Alberta Canada
- Fuyi Li
- School of Geographical Sciences Northeast Normal University Changchun Jilin China
- Liwei Li
- Department of Gastroenterology The Second Affiliated Hospital of Guangxi Medical University Nanning Guangxi China
- Miao Li
- Synaura Biotechnology (Shanghai) Co., Ltd. Shanghai China
- Xin Li
- School of Public Health University of Michigan Ann Arbor Michigan USA
- Ye Li
- Institute of Soil Science, Chinese Academy of Sciences Nanjing Jiangsu China
- Zheng‐Tao Li
- School of Art and Archaeology of Zhejiang University Zhejiang China
- Jing Liang
- College of Animal Science and Technology Guangxi University Nanning China
- Yongxin Lin
- Fujian Provincial Key Laboratory for Subtropical Resources and Environment Fujian Normal University Fuzhou China
- Changzhen Liu
- College of Energy and Environmental Engineering Hebei University of Engineering Handan Hebei China
- Danni Liu
- HaploX Biotechnology Shenzhen China
- Fengqin Liu
- College of Life Sciences Henan Agricultural University Zhengzhou China
- Jia Liu
- College of Life Science Nankai University Tianjin China
- Tianrui Liu
- Jiangxi Province Key Laboratory of Sustainable Utilization of Traditional Chinese Medicine Resources, Institute of Traditional Chinese Medicine Health Industry, China Academy of Chinese Medical Sciences Jiangxi China
- Tingting Liu
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital Capital Medical University Beijing China
- Xinyuan Liu
- State Key Laboratory of Tea Plant Biology and Utilization Anhui Agricultural University Hefei Anhui China
- Yaqun Liu
- School of Life Sciences and Food Technology Hanshan Normal University Chaozhou China
- Bangyan Liu
- Tsinghua University Beijing China
- Minghao Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences Beijing China
- Wenbo Lou
- College of Animal Science and Technology Jilin Agricultural University Changchun Jilin China
- Yaning Luan
- The College of Forestry Beijing Forestry University Beijing China
- Yuanyuan Luo
- State Key Laboratory of Tea Plant Biology and Utilization Anhui Agricultural University Hefei Anhui China
- Hujie Lv
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China
- Tengfei Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro‐Ecosystems, Centre for Grassland Microbiome, College of Pastoral Agriculture Science and Technology Lanzhou University Lanzhou Gansu China
- Zongjiong Mai
- Department of Oncology The Fifth Affiliated Hospital of Sun Yat‐sen University Zhuhai Guangdong China
- Jiayuan Mo
- College of Animal Science and Technology Guangxi University Nanning China
- Dongze Niu
- National‐Local Joint Engineering Research Center of Biomass Refining and High‐Quality Utilization, Institute of Urban and Rural Mining Changzhou University Changzhou Jiangsu China
- Zhuo Pan
- Department of Pathology Affiliated Cancer Hospital of Zhengzhou University Zhengzhou China
- Heyuan Qi
- Institute of Microbiology, Chinese Academy of Sciences Beijing China
- Zhanyao Shi
- College of Water Sciences Beijing Normal University Beijing China
- Chunjiao Song
- Deyang People's Hospital Deyang Sichuan China
- Fuxiang Sun
- New Direction Biotechnology (Tianjin) Co., Ltd Tianjin China
- Yan Sun
- College of Energy and Environmental Engineering, Hebei Key Laboratory of Air Pollution Cause and Impact Hebei University of Engineering Handan China
- Sihui Tian
- Institute of Botany, Chinese Academy of Sciences Beijing China
- Xiulin Wan
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China
- Guoliang Wang
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences Beijing China
- Hongyang Wang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences Jiangsu China
- Hongyu Wang
- College of Animal Science Anhui Science and Technology University Chuzhou China
- Huanhuan Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing China
- Jing Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences Beijing China
- Jun Wang
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention Beijing China
- Kang Wang
- College of Animal Science and Technology Yangzhou University Yangzhou Jiangsu China
- Leli Wang
- Key Laboratory of Agro‐Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences Changsha China
- Shao‐kun Wang
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry Beijing China
- Xinlong Wang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital Capital Medical University Beijing China
- Yao Wang
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China
- Zufei Xiao
- State Key Laboratory for Ecological Security of Regions and Cities, Institute of Urban Environment, Chinese Academy of Sciences Xiamen China
- Huichun Xing
- Center of Liver Diseases Division 3, Beijing Ditan Hospital Capital Medical University Beijing China
- Yifan Xu
- Center of Liver Diseases Division 3, Beijing Ditan Hospital Capital Medical University Beijing China
- Shu‐yan Yan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Invasive Alien Species Control of Ministry of Agriculture and Rural Affairs, Institute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing China
- Li Yang
- Sansure Biotech Incorporation Changsha Hunan China
- Song Yang
- Center of Liver Diseases Division 3, Beijing Ditan Hospital Capital Medical University Beijing China
- Yuanming Yang
- Guangzhou University of Chinese Medicine Guangzhou China
- Xiaofang Yao
- Key Laboratory of Agro‐Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences Changsha China
- Salsabeel Yousuf
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China
- Hao Yu
- Institute of Marine Biology and Pharmacology, Ocean College Zhejiang University Zhoushan Zhejiang China
- Yu Lei
- Key Laboratory of Livestock Biology Northwest A&F University Yangling Shaanxi China
- Zhengrong Yuan
- College of Biological Sciences and Technology Beijing Forestry University Beijing China
- Meiyin Zeng
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China
- Chunfang Zhang
- Institute of Marine Biology and Pharmacology, Ocean College Zhejiang University Zhoushan Zhejiang China
- Chunge Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences Beijing China
- Huimin Zhang
- School of Food Science and Technology Shihezi University Shihezi Xinjiang China
- Jing Zhang
- HaploX Biotechnology Shenzhen China
- Na Zhang
- College of Biochemical Engineering Beijing Union University Beijing China
- Tianyuan Zhang
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China
- Yi‐Bo Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Invasive Alien Species Control of Ministry of Agriculture and Rural Affairs, Institute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing China
- Yupeng Zhang
- College of Resources and Environmental Sciences Henan Agricultural University Zhengzhou China
- Zheng Zhang
- Tea Research Institute, Chinese Academy of Agricultural Sciences Hangzhou Zhejiang China
- Mingda Zhou
- College of Environmental Science and Engineering Tongji University Shanghai China
- Yuanping Zhou
- Zhanjiang Key Laboratory of Human Microecology and Clinical Translation Research, the Marine Biomedical Research Institute, College of Basic Medicine Guangdong Medical University Zhanjiang Guangdong China
- Chengshuai Zhu
- School of Art and Archaeology of Zhejiang University Zhejiang China
- Lin Zhu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology Harbin China
- Yue Zhu
- School of Ecology, Environment and Resources Guangdong University of Technology Guangzhou Guangdong China
- Zhihao Zhu
- Zhanjiang Key Laboratory of Human Microecology and Clinical Translation Research, the Marine Biomedical Research Institute, College of Basic Medicine Guangdong Medical University Zhanjiang Guangdong China
- Hongqin Zou
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences Beijing China
- Anna Zuo
- School of Traditional Chinese Medicine Southern Medical University Guangzhou Guangdong China
- Wenxuan Dong
- Department of Animal Sciences Purdue University West Lafayette Indiana USA
- Tao Wen
- College of Resource and Environmental Sciences Nanjing Agricultural University Nanjing Jiangsu China
- Shifu Chen
- HaploX Biotechnology Shenzhen China
- Guoliang Li
- Jiangxi Provincial Key Laboratory of Conservation Biology, College of Forestry Jiangxi Agricultural University Nanchang Jiangxi China
- Yunyun Gao
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China
- Yong‐Xin Liu
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China
- DOI
- https://doi.org/10.1002/imt2.70001
- Journal volume & issue
-
Vol. 4,
no. 1
pp. n/a – n/a
Abstract
Abstract Shotgun metagenomics has become a pivotal technology in microbiome research, enabling in‐depth analysis of microbial communities at both the high‐resolution taxonomic and functional levels. This approach provides valuable insights of microbial diversity, interactions, and their roles in health and disease. However, the complexity of data processing and the need for reproducibility pose significant challenges to researchers. To address these challenges, we developed EasyMetagenome, a user‐friendly pipeline that supports multiple analysis methods, including quality control and host removal, read‐based, assembly‐based, and binning, along with advanced genome analysis. The pipeline also features customizable settings, comprehensive data visualizations, and detailed parameter explanations, ensuring its adaptability across a wide range of data scenarios. Looking forward, we aim to refine the pipeline by addressing host contamination issues, optimizing workflows for third‐generation sequencing data, and integrating emerging technologies like deep learning and network analysis, to further enhance microbiome insights and data accuracy. EasyMetageonome is freely available at https://github.com/YongxinLiu/EasyMetagenome.
Keywords
