EasyMetagenome: A user-friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research
文献类型： 外文期刊
作者： Bai, Defeng 1 ; Chen, Tong 2 ; Xun, Jiani 1 ; Ma, Chuang 1 ; Luo, Hao 1 ; Yang, Haifei 1 ; Cao, Chen 5 ; Cao, Xiaofeng 6 ; Cui, Jianzhou 7 ; Deng, Yuan-Ping 8 ; Deng, Zhaochao 9 ; Dong, Wenxin 10 ; Dong, Wenxue 11 ; Du, Juan 12 ; Fang, Qunkai 13 ; Fang, Wei 14 ; Fang, Yue 15 ; Fu, Fangtian 16 ; Fu, Min 17 ; Fu, Yi-Tian 18 ; Gao, He 19 ; Ge, Jingping 20 ; Gong, Qinglong 21 ; Gu, Lunda 22 ; Guo, Peng 23 ; Guo, Yuhao 20 ; Hai, Tang 24 ; Liu, Hao 25 ; He, Jieqiang 26 ; He, Zi-Yang 27 ; Hou, Huiyu 1 ; Huang, Can 28 ; Ji, Shuai 29 ; Jiang, ChangHai 30 ; Jiang, Gui-Lai 31 ; Jiang, Lingjuan 32 ; Jin, Ling N. 33 ; Kan, Yuhe 34 ; Kang, Da 35 ; Kou, Jin 36 ; Lam, Ka-Lung 37 ; Li, Changchao 33 ; Li, Chong 38 ; Li, Fuyi 39 ; Li, Liwei 40 ; Li, Miao 41 ; Li, Xin 42 ; Li, Ye 43 ; Li, Zheng-Tao 44 ; Liang, Jing 45 ; Lin, Yongxin 46 ; Liu, Changzhen 47 ; Liu, Danni 48 ; Liu, Fengqin 49 ; Liu, Jia 50 ; Liu, Tianrui 51 ; Liu, Tingting 52 ; Liu, Xinyuan 53 ; Liu, Yaqun 54 ; Liu, Bangyan 55 ; Liu, Minghao 56 ; Lou, Wenbo 21 ; Luan, Yaning 15 ; Luo, Yuanyuan 53 ; Lv, Hujie 1 ; Ma, Tengfei 58 ; Mai, Zongjiong 59 ; Mo, Jiayuan 45 ; Niu, Dongze 60 ; Pan, Zhuo 61 ; Qi, Heyuan 62 ; Shi, Zhanyao 63 ; Song, Chunjiao 64 ; Sun, Fuxiang 65 ; Sun, Yan 66 ; Tian, Sihui 67 ; Wan, Xiulin 1 ; Wang, Guoliang 68 ; Wang, Hongyang 69 ; Wang, Hongyu 70 ; Wang, Huanhuan 71 ; Wang, Jing 72 ; Wang, Jun 73 ; Wang, Kang 74 ; Wang, Leli 75 ; Wang, Shao-kun 76 ; Wang, Xinlong 52 ; Wang, Yao 1 ; Xiao, Zufei 77 ; Xing, Huichun 78 ; Xu, Yifan 78 ; Yan, Shu-yan 79 ; Yang, Li 22 ; Yang, Song 78 ; Yang, Yuanming 80 ; Yao, Xiaofang 75 ; Yousuf, Salsabeel 1 ; Yu, Hao 9 ; Lei, Yu 81 ; Yuan, Zhengrong 82 ; Zeng, Meiyin 1 ; Zhang, Chunfang 9 ; Zhang, Chunge 83 ; Zhang, Huimin 84 ; Zhang, Jing 48 ; Zhang, Na 85 ; Zhang, Tianyuan 1 ; Zhang, Yi-Bo 79 ; Zhang, Yupeng 86 ; Zhang, Zheng 87 ; Zhou, Mingda 88 ; Zhou, Yuanping 89 ; Zhu, Chengshuai 44 ; Zhu, Lin 90 ; Zhu, Yue 91 ; Zhu, Zhihao 89 ; Zou, Hongqin 92 ; Zuo, Anna 93 ; Dong, Wenxuan 94 ; Wen, Tao 95 ; Chen, Shifu 48 ; Li, Guoliang 98 ; Gao, Yunyun 1 ; Liu, Yong-Xin 1 ;
作者机构： 1.Chinese Acad Agr Sci, Agr Genom Inst, Genome Anal Lab, Minist Agr & Rural Affairs, Shenzhen, Guangdong, Peoples R China
2.China Acad Chinese Med Sci, Natl Resource Ctr Chinese Mat Med, State Key Lab Qual Ensurance & Sustainable Use Da, Beijing, Peoples R China
3.Anhui Agr Univ, Sch Hort, Hefei, Peoples R China
4.Qingdao Agr Univ, Coll Life Sci, Qingdao, Peoples R China
5.Nanjing Med Univ, Sch Biomed Engn & Informat, Key Lab Bio Elect Environm & Adv Med Theranost, Nanjing, Jiangsu, Peoples R China
6.Tsinghua Univ, Sch Environm, Ctr Water & Ecol, State Key Joint Lab Environm Simulat & Pollut Con, Beijing, Peoples R China
7.Natl Univ Singapore, Yong Loo Lin Sch Med, Immunol Translat Res Programme, Singapore, Singapore
8.Hunan Agr Univ, Coll Vet Med, Res Ctr Parasites & Vectors, Changsha, Hunan, Peoples R China
9.Zhejiang Univ, Inst Marine Biol & Pharmacol, Ocean Coll, Zhoushan, Zhejiang, Peoples R China
10.Minist Agr & Rural Affairs, Agroenvironm Protect Inst, Tianjin, Peoples R China
11.Xizang Minzu Univ, Key Lab Mol Genet Mech & Intervent Res High Altit, Sch Med, Xianyang, Peoples R China
12.Karolinska Inst, Dept Microbiol Tumor & Cell Biol, Stockholm, Sweden
13.Zhejiang Univ Technol, Coll Environm, Hangzhou, Peoples R China
14.Zhejiang Agr & Forestry Univ, Coll Environm & Resource Sci, Hangzhou, Peoples R China
15.Beijing Forestry Univ, Coll Forestry, Beijing, Peoples R China
16.Hangzhou VicrobX Biotech Co Ltd, Dept Bioinformat, Hangzhou, Zhejiang, Peoples R China
17.Anhui Agr Univ, Coll Plant Protect, Anhui Prov Key Lab Integrated Pest Management Cro, Hefei, Peoples R China
18.Cent South Univ, Xiangya Sch Basic Med, Changsha, Hunan, Peoples R China
19.Guangdong Acad Sci, Inst Microbiol, Guangzhou, Guangdong, Peoples R China
20.Heilongjiang Univ, Sch Life Sci, Engn Res Ctr Agr Microbiol Technol, Minist Educ, Harbin, Peoples R China
21.Jilin Agr Univ, Coll Anim Sci & Technol, Changchun, Jilin, Peoples R China
22.Sansure Biotech Incorp, Changsha, Hunan, Peoples R China
23.Hebei Univ Sci & Technol, Sch Food Sci & Biol, Shijiazhuang, Hebei, Peoples R China
24.Shanxi Datong Univ, Sch Life Sci, Datong, Peoples R China
25.Xian Jiaotong Liverpool Univ, Dept Environm Hlth Sci, Suzhou, Jiangsu, Peoples R China
26.Northwest A&F Univ, Coll Hort, Yangling, Shaanxi, Peoples R China
27.Univ Melbourne, School Agr Food & Ecosyst Sci, Fac Sci, Melbourne, Vic, Australia
28.Univ Tokyo, Grad Sch Frontier Sci, Kashiwa, Chiba, Japan
29.Univ Helsinki, Inst Biotechnol, Helsinki Inst Life Sci, Helsinki, Finland
30.Shanghai Maritime Univ, Shanghai, Peoples R China
31.Soochow Univ, Suzhou Med Coll, Suzhou, Jiangsu, Peoples R China
32.Peking Union Med Coll Hosp, Inst Clin Med, Biomarker Discovery & Validat Facil, Beijing, Peoples R China
33.Hong Kong Polytech Univ, Dept Civil & Environm Engn, Hong Kong, Peoples R China
34.Weifang Univ, Coll Biol & Oceanog, Weifang, Shandong, Peoples R China
35.Beijing Univ Technol, Coll Environm Sci & Engn, Beijing, Peoples R China
36.Lanzhou Jiaotong Univ, Coll Environm & Municipal Engn, Lanzhou, Peoples R China
37.Chinese Univ Hong Kong, Sch Life Sci, Shatin, Hong Kong, Peoples R China
38.Univ Alberta, Dept Renewable Resources, Edmonton, AB, Canada
39.Northeast Normal Univ, Sch Geog Sci, Changchun, Jilin, Peoples R China
40.Guangxi Med Univ, Dept Gastroenterol, Affiliated Hosp 2, Nanning, Guangxi, Peoples R China
41.Synaura Biotechnol Shanghai Co Ltd, Shanghai, Peoples R China
42.Univ Michigan, Sch Publ Hlth, Ann Arbor, MI USA
43.Chinese Acad Sci, Inst Soil Sci, Nanjing, Jiangsu, Peoples R China
44.Zhejiang Univ, Sch Art & Archaeol, Hangzhou, Zhejiang, Peoples R China
45.Guangxi Univ, Coll Anim Sci & Technol, Nanning, Peoples R China
46.Fujian Normal Univ, Fujian Prov Key Lab Subtrop Resources & Environm, Fuzhou, Peoples R China
47.Hebei Univ Engn, Coll Energy & Environm Engn, Handan, Hebei, Peoples R China
48.HaploX Biotechnol, Shenzhen, Peoples R China
49.Henan Agr Univ, Coll Life Sci, Zhengzhou, Peoples R China
50.Nankai Univ, Coll Life Sci, Tianjin, Peoples R China
51.China Acad Chinese Med Sci, Jiangxi Prov Key Lab Sustainable Utilizat Tradit, Inst Tradit Chinese Med Hlth Ind, Beijing, Jiangxi, Peoples R China
52.Capital Med Univ, Beijing Ditan Hosp, Inst Infect Dis, Beijing Key Lab Emerging Infect Dis, Beijing, Peoples R China
53.Anhui Agr Univ, State Key Lab Tea Plant Biol & Utilizat, Hefei, Anhui, Peoples R China
54.Hanshan Normal Univ, Sch Life Sci & Food Technol, Chaozhou, Peoples R China
55.Tsinghua Univ, Beijing, Peoples R China
56.Chinese Acad Sci, Inst Microbiol, State Key Lab Microbial Resources, Beijing, Peoples R China
57.Imperial Coll London, Dept Life Sci, London, England
58.Lanzhou Univ, Coll Pastoral Agr Sci & Technol, Ctr Grassland Microbiome, State Key Lab Herbage Improvement & Grassland Agr, Lanzhou, Gansu, Peoples R China
59.Sun Yat Sen Univ, Dept Oncol, Affiliated Hosp 5, Zhuhai, Guangdong, Peoples R China
60.Changzhou Univ, Inst Urban & Rural Min, Natl Local Joint Engn Res Ctr Biomass Refining &, Changzhou, Jiangsu, Peoples R China
61.Zhengzhou Univ, Dept Pathol, Affiliated Canc Hosp, Zhengzhou, Peoples R China
62.Chinese Acad Sci, Inst Microbiol, Beijing, Peoples R China
63.Beijing Normal Univ, Coll Water Sci, Beijing, Peoples R China
64.Deyang Peoples Hosp, Deyang, Sichuan, Peoples R China
65.New Direct Biotechnol Tianjin Co Ltd, Tianjin, Peoples R China
66.Hebei Univ Engn, Coll Energy & Environm Engn, Hebei Key Lab Air Pollut Cause & Impact, Handan, Peoples R China
67.Chinese Acad Sci, Inst Bot, Beijing, Peoples R China
68.Beijing Acad Agr & Forestry Sci, Inst Biotechnol, Beijing, Peoples R China
69.China Acad Chinese Med Sci, Natl Resource Ctr Chinese Mat Med, Beijing, Jiangsu, Peoples R China
70.Anhui Sci & Technol Univ, Coll Anim Sci, Chuzhou, Peoples R China
71.Chinese Acad Agr Sci, Inst Plant Protect, State Key Lab Biol Plant Dis & Insect Pests, Beijing, Peoples R China
72.Chinese Res Inst Environm Sci, State Key Lab Environm Criteria & Risk Assessment, Beijing, Peoples R China
73.Natl Inst Environm Hlth, Chinese Ctr Dis Control & Prevent, China CDC Key Lab Environm & Populat Hlth, Beijing, Peoples R China
74.Yangzhou Univ, Coll Anim Sci & Technol, Yangzhou, Jiangsu, Peoples R China
75.Chinese Acad Sci, Inst Subtrop Agr, Key Lab Agro Ecol Processes Subtrop Region, Changsha, Peoples R China
76.Chinese Acad Forestry, Inst Ecol Conservat & Restorat, Beijing, Peoples R China
77.Chinese Acad Sci, Inst Urban Environm, State Key Lab Ecol Secur Reg & Cities, Xiamen, Peoples R China
78.Capital Med Univ, Beijing Ditan Hosp, Ctr Liver Dis Div, Beijing, Peoples R China
79.Chinese Acad Agr Sci, Inst Plant Protect, State Key Lab Biol Plant Dis & Insect Pests, Key Lab Invas Alien Species Control,Minist Agr &, Beijing, Peoples R China
80.Guangzhou Univ Chinese Med, Guangzhou, Peoples R China
81.Northwest A&F Univ, Key Lab Livestock Biol, Yangling, Shaanxi, Peoples R China
82.Beijing Forestry Univ, Coll Biol Sci & Technol, Beijing, Peoples R China
83.Chinese Acad Sci, Inst Microbiol, CAS Key Lab Pathogen Microbiol & Immunol, Beijing, Peoples R China
84.Shihezi Univ, Sch Food Sci & Technol, Shihezi, Xinjiang, Peoples R China
85.Beijing Union Univ, Coll Biochem Engn, Beijing, Peoples R China
86.Henan Agr Univ, Coll Resources & Environm Sci, Zhengzhou, Peoples R China
87.Chinese Acad Agr Sci, Tea Res Inst, Hangzhou, Zhejiang, Peoples R China
88.Tongji Univ, Coll Environm Sci & Engn, Shanghai, Peoples R China
89.Guangdong Med Univ, Marine Biomed Res Inst, Coll Basic Med, Zhanjiang Key Lab Human Microecol & Clin Translat, Zhanjiang, Guangdong, Peoples R China
90.Harbin Inst Technol, Sch Environm, State Key Lab Urban Water Resource & Environm, Harbin, Peoples R China
91.Guangdong Univ Technol, Sch Ecol Environm & Resources, Guangzhou, Guangdong, Peoples R China
92.Chinese Acad Agr Sci, Inst Agr Resources & Reg Planning, Beijing, Peoples R China
93.Southern Med Univ, Sch Tradit Chinese Med, Guangzhou, Guangdong, Peoples R China
94.Purdue Univ, Dept Anim Sci, W Lafayette, IN USA
95.Nanjing Agr Univ, Coll Resource & Environm Sci, Nanjing, Jiangsu, Peoples R China
96.Gannan Med Univ, LifeX Inst, Sch Med Technol, Ganzhou, Peoples R China
97.City Univ Macau, Fac Data Sci, Macau, Peoples R China
98.Jiangxi Agr Univ, Coll Forestry, Jiangxi Prov Key Lab Conservat Biol, Nanchang, Jiangxi, Peoples R China
关键词： metagenome; microbiome; microbiota; pipeline; visualization
期刊名称：IMETA （ 影响因子：33.2； 五年影响因子：33.2 ）
ISSN： 2770-5986
年卷期： 2025 年 4 卷 1 期
页码：
收录情况： SCI
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.
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