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EasyMetagenome: A user-friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research

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机构: [1]Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China. [2]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. [3]School of Horticulture Anhui Agricultural University Hefei China. [4]College of Life Sciences Qingdao Agricultural University Qingdao China. [5]Key Laboratory for Bio-Electromagnetic Environment and Advanced Medical Theranostics, School of Biomedical Engineering and Informatics Nanjing Medical University Nanjing Jiangsu China. [6]Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment Tsinghua University Beijing China. [7]Immunology Translational Research Programme, Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore. [8]Research Center for Parasites and Vectors, College of Veterinary Medicine Hunan Agricultural University Changsha Hunan China. [9]Institute of Marine Biology and Pharmacology, Ocean College Zhejiang University Zhoushan Zhejiang China. [10]Agro-Environmental Protection Institute Ministry of Agriculture and Rural Affairs Tianjin China. [11]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. [12]Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology Stockholm Sweden. [13]College of Environment Zhejiang University of Technology Hangzhou China. [14]College of Environmental and Resource Sciences Zhejiang Agriculture and Forestry University Hangzhou China. [15]The College of Forestry Beijing Forestry University Beijing China. [16]Department of Bioinformatics, Hangzhou VicrobX Biotech Co., Ltd Hangzhou Zhejiang China. [17]Anhui Province Key Laboratory of Integrated Pest Management on Crops, College of Plant Protection Anhui Agricultural University Hefei China. [18]Xiangya School of Basic Medicine Central South University Changsha Hunan China. [19]Institute of Microbiology,Guangdong Academy of Sciences Guangzhou Guangdong China. [20]Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, School of Life Sciences Heilongjiang University Harbin China. [21]College of Animal Science and Technology Jilin Agricultural University Changchun Jilin China. [22]Sansure Biotech Incorporation Changsha Hunan China. [23]School of Food Science and Biology Hebei University of Science and Technology Shijiazhuang Hebei China. [24]School of Life Sciences Shanxi Datong University Datong China. [25]Department of Health & Environmental Sciences, Xi'an Jiaotong‐ Liverpool University, Suzhou, Jiangsu, China [26]College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China [27]School of Agriculture, Food and Ecosystem Sciences, Faculty of Science The University of Melbourne VIC Australia. [28]Graduate School of Frontier Sciences The University of Tokyo Kashiwa-shi, Chiba Japan. [29]Institute of Biotechnology, Helsinki Institute of Life Science University of Helsinki Helsinki Finland. [30]Shanghai Maritime University Shanghai China. [31]Suzhou Medical College Soochow University Suzhou Jiangsu China. [32]Biomarker Discovery and Validation Facility, Institute of Clinical Medicine, Peking Union Medical College Hospital Beijing China. [33]Department of Civil and Environmental Engineering The Hong Kong Polytechnic University Hong Kong China. [34]College of Biology and Oceanography Weifang University Weifang Shandong China. [35]College of Environmental Science and Engineering Beijing University of Technology Beijing China. [36]College of Environmental and Municipal Engineering Lanzhou Jiaotong University Lanzhou China. [37]School of Life Sciences The Chinese University of Hong Kong Shatin, Hong Kong China. [38]Department of Renewable Resources University of Alberta Edmonton Alberta Canada. [39]School of Geographical Sciences Northeast Normal University Changchun Jilin China. [40]Department of Gastroenterology The Second Affiliated Hospital of Guangxi Medical University Nanning Guangxi China. [41]Synaura Biotechnology (Shanghai) Co., Ltd. Shanghai China. [42]School of Public Health University of Michigan Ann Arbor Michigan USA. [43]Institute of Soil Science, Chinese Academy of Sciences Nanjing Jiangsu China. [44]School of Art and Archaeology of Zhejiang University Zhejiang China. [45]College of Animal Science and Technology Guangxi University Nanning China. [46]Fujian Provincial Key Laboratory for Subtropical Resources and Environment Fujian Normal University Fuzhou China. [47]College of Energy and Environmental Engineering Hebei University of Engineering Handan Hebei China. [48]HaploX Biotechnology Shenzhen China. [49]College of Life Sciences Henan Agricultural University Zhengzhou China. [50]College of Life Science Nankai University Tianjin China. [51]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. [52]Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital Capital Medical University Beijing China. [53]State Key Laboratory of Tea Plant Biology and Utilization Anhui Agricultural University Hefei Anhui China. [54]School of Life Sciences and Food Technology Hanshan Normal University Chaozhou China. [55]Tsinghua University Beijing China. [56]State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences Beijing China. [57]Department of Life Sciences, Imperial College of London London UK. [58]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. [59]Department of Oncology The Fifth Affiliated Hospital of Sun Yat-sen University Zhuhai Guangdong China. [60]National-Local Joint Engineering Research Center of Biomass Refining and High-Quality Utilization, Institute of Urban and Rural Mining Changzhou University Changzhou Jiangsu China. [61]Department of Pathology Affiliated Cancer Hospital of Zhengzhou University Zhengzhou China. [62]Institute of Microbiology, Chinese Academy of Sciences Beijing China. [63]College of Water Sciences Beijing Normal University Beijing China. [64]Deyang People's Hospital Deyang Sichuan China. [65]New Direction Biotechnology (Tianjin) Co., Ltd Tianjin China. [66]College of Energy and Environmental Engineering, Hebei Key Laboratory of Air Pollution Cause and Impact Hebei University of Engineering Handan China. [67]Institute of Botany, Chinese Academy of Sciences Beijing China. [68]Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences Beijing China. [69]National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences Jiangsu China. [70]College of Animal Science Anhui Science and Technology University Chuzhou China. [71]State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing China. [72]State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences Beijing China. [73]China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention Beijing China. [74]College of Animal Science and Technology Yangzhou University Yangzhou Jiangsu China. [75]Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences Changsha China. [76]Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry Beijing China. [77]State Key Laboratory for Ecological Security of Regions and Cities, Institute of Urban Environment, Chinese Academy of Sciences Xiamen China. [78]Center of Liver Diseases Division 3, Beijing Ditan Hospital Capital Medical University Beijing China. [79]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. [80]Guangzhou University of Chinese Medicine Guangzhou China. [81]Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, China [82]College of Biological Sciences and Technology Beijing Forestry University Beijing China. [83]CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences Beijing China. [84]School of Food Science and Technology Shihezi University Shihezi Xinjiang China. [85]College of Biochemical Engineering Beijing Union University Beijing China. [86]College of Resources and Environmental Sciences Henan Agricultural University Zhengzhou China. [87]Tea Research Institute, Chinese Academy of Agricultural Sciences Hangzhou Zhejiang China. [88]College of Environmental Science and Engineering Tongji University Shanghai China. [89]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. [90]State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology Harbin China. [91]School of Ecology, Environment and Resources Guangdong University of Technology Guangzhou Guangdong China. [92]Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences Beijing China. [93]School of Traditional Chinese Medicine Southern Medical University Guangzhou Guangdong China. [94]Department of Animal Sciences Purdue University West Lafayette Indiana USA. [95]College of Resource and Environmental Sciences Nanjing Agricultural University Nanjing Jiangsu China. [96]LifeX Institute, School of Medical Technology Gannan Medical University Ganzhou China. [97]Faculty of Data Science City University of Macau Macau China. [98]Jiangxi Provincial Key Laboratory of Conservation Biology, College of Forestry Jiangxi Agricultural University Nanchang Jiangxi China.
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关键词: metagenome microbiome microbiota pipeline visualization

摘要:
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.© 2025 The Author(s). iMeta published by John Wiley & Sons Australia, Ltd on behalf of iMeta Science.

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出版当年[2025]版:
大类 | 1 区 生物学
小类 | 1 区 微生物学
最新[2025]版:
大类 | 1 区 生物学
小类 | 1 区 微生物学
第一作者:
第一作者机构: [1]Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China.
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通讯作者:
通讯机构: [48]HaploX Biotechnology Shenzhen China. [96]LifeX Institute, School of Medical Technology Gannan Medical University Ganzhou China. [97]Faculty of Data Science City University of Macau Macau China.
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