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Main Authors:	Bai, Defeng, Chen, Tong, Xun, Jiani, Ma, Chuang, Luo, Hao, Yang, Haifei, Cao, Chen, Cao, Xiaofeng, Cui, Jianzhou, Deng, Yuan-Ping, Deng, Zhaochao, Dong, Wenxin, Dong, Wenxue, Du, Juan, Fang, Qunkai, Fang, Wei, Fang, Yue, Fu, Fangtian, Fu, Min, Fu, Yi-Tian, Gao, He, Ge, Jingping, Gong, Qinglong, Gu, Lunda, Guo, Peng, Guo, Yuhao, Hai, Tang, Liu, Hao, He, Jieqiang, He, Zi-Yang, Hou, Huiyu, Huang, Can, Ji, Shuai, Jiang, ChangHai, Jiang, Gui-Lai, Jiang, Lingjuan, Jin, Ling N, Kan, Yuhe, Kang, Da, Kou, Jin, Lam, Ka-Lung, Li, Changchao, Li, Chong, Li, Fuyi, Li, Liwei, Li, Miao, Li, Xin, Li, Ye, Li, Zheng-Tao, Liang, Jing, Lin, Yongxin, Liu, Changzhen, Liu, Danni, Liu, Fengqin, Liu, Jia, Liu, Tianrui, Liu, Tingting, Liu, Xinyuan, Liu, Yaqun, Liu, Bangyan, Liu, Minghao, Lou, Wenbo, Luan, Yaning, Luo, Yuanyuan, Lv, Hujie, Ma, Tengfei, Mai, Zongjiong, Mo, Jiayuan, Niu, Dongze, Pan, Zhuo, Qi, Heyuan, Shi, Zhanyao, Song, Chunjiao, Sun, Fuxiang, Sun, Yan, Tian, Sihui, Wan, Xiulin, Wang, Guoliang, Wang, Hongyang, Wang, Hongyu, Wang, Huanhuan, Wang, Jing, Wang, Jun, Wang, Kang, Wang, Leli, Wang, Shao-Kun, Wang, Xinlong, Wang, Yao, Xiao, Zufei, Xing, Huichun, Xu, Yifan, Yan, Shu-Yan, Yang, Li, Yang, Song, Yang, Yuanming, Yao, Xiaofang, Yousuf, Salsabeel, Yu, Hao, Lei, Yu, Yuan, Zhengrong, Zeng, Meiyin, Zhang, Chunfang, Zhang, Chunge, Zhang, Huimin, Zhang, Jing, Zhang, Na, Zhang, Tianyuan, Zhang, Yi-Bo, Zhang, Yupeng, Zhang, Zheng, Zhou, Mingda, Zhou, Yuanping, Zhu, Chengshuai, Zhu, Lin, Zhu, Yue, Zhu, Zhihao, Zou, Hongqin, Zuo, Anna, Dong, Wenxuan, Wen, Tao, Chen, Shifu, Li, Guoliang, Gao, Yunyun, Liu, Yong-Xin
Format:	Artículo científico
Language:	en
Published:	iMeta 2025
Online Access:	https://pubmed.ncbi.nlm.nih.gov/40027489/
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_version_	1868266237303193600
author	Bai, Defeng Chen, Tong Xun, Jiani Ma, Chuang Luo, Hao Yang, Haifei Cao, Chen Cao, Xiaofeng Cui, Jianzhou Deng, Yuan-Ping Deng, Zhaochao Dong, Wenxin Dong, Wenxue Du, Juan Fang, Qunkai Fang, Wei Fang, Yue Fu, Fangtian Fu, Min Fu, Yi-Tian Gao, He Ge, Jingping Gong, Qinglong Gu, Lunda Guo, Peng Guo, Yuhao Hai, Tang Liu, Hao He, Jieqiang He, Zi-Yang Hou, Huiyu Huang, Can Ji, Shuai Jiang, ChangHai Jiang, Gui-Lai Jiang, Lingjuan Jin, Ling N Kan, Yuhe Kang, Da Kou, Jin Lam, Ka-Lung Li, Changchao Li, Chong Li, Fuyi Li, Liwei Li, Miao Li, Xin Li, Ye Li, Zheng-Tao Liang, Jing Lin, Yongxin Liu, Changzhen Liu, Danni Liu, Fengqin Liu, Jia Liu, Tianrui Liu, Tingting Liu, Xinyuan Liu, Yaqun Liu, Bangyan Liu, Minghao Lou, Wenbo Luan, Yaning Luo, Yuanyuan Lv, Hujie Ma, Tengfei Mai, Zongjiong Mo, Jiayuan Niu, Dongze Pan, Zhuo Qi, Heyuan Shi, Zhanyao Song, Chunjiao Sun, Fuxiang Sun, Yan Tian, Sihui Wan, Xiulin Wang, Guoliang Wang, Hongyang Wang, Hongyu Wang, Huanhuan Wang, Jing Wang, Jun Wang, Kang Wang, Leli Wang, Shao-Kun Wang, Xinlong Wang, Yao Xiao, Zufei Xing, Huichun Xu, Yifan Yan, Shu-Yan Yang, Li Yang, Song Yang, Yuanming Yao, Xiaofang Yousuf, Salsabeel Yu, Hao Lei, Yu Yuan, Zhengrong Zeng, Meiyin Zhang, Chunfang Zhang, Chunge Zhang, Huimin Zhang, Jing Zhang, Na Zhang, Tianyuan Zhang, Yi-Bo Zhang, Yupeng Zhang, Zheng Zhou, Mingda Zhou, Yuanping Zhu, Chengshuai Zhu, Lin Zhu, Yue Zhu, Zhihao Zou, Hongqin Zuo, Anna Dong, Wenxuan Wen, Tao Chen, Shifu Li, Guoliang Gao, Yunyun Liu, Yong-Xin
author_facet	Bai, Defeng Chen, Tong Xun, Jiani Ma, Chuang Luo, Hao Yang, Haifei Cao, Chen Cao, Xiaofeng Cui, Jianzhou Deng, Yuan-Ping Deng, Zhaochao Dong, Wenxin Dong, Wenxue Du, Juan Fang, Qunkai Fang, Wei Fang, Yue Fu, Fangtian Fu, Min Fu, Yi-Tian Gao, He Ge, Jingping Gong, Qinglong Gu, Lunda Guo, Peng Guo, Yuhao Hai, Tang Liu, Hao He, Jieqiang He, Zi-Yang Hou, Huiyu Huang, Can Ji, Shuai Jiang, ChangHai Jiang, Gui-Lai Jiang, Lingjuan Jin, Ling N Kan, Yuhe Kang, Da Kou, Jin Lam, Ka-Lung Li, Changchao Li, Chong Li, Fuyi Li, Liwei Li, Miao Li, Xin Li, Ye Li, Zheng-Tao Liang, Jing Lin, Yongxin Liu, Changzhen Liu, Danni Liu, Fengqin Liu, Jia Liu, Tianrui Liu, Tingting Liu, Xinyuan Liu, Yaqun Liu, Bangyan Liu, Minghao Lou, Wenbo Luan, Yaning Luo, Yuanyuan Lv, Hujie Ma, Tengfei Mai, Zongjiong Mo, Jiayuan Niu, Dongze Pan, Zhuo Qi, Heyuan Shi, Zhanyao Song, Chunjiao Sun, Fuxiang Sun, Yan Tian, Sihui Wan, Xiulin Wang, Guoliang Wang, Hongyang Wang, Hongyu Wang, Huanhuan Wang, Jing Wang, Jun Wang, Kang Wang, Leli Wang, Shao-Kun Wang, Xinlong Wang, Yao Xiao, Zufei Xing, Huichun Xu, Yifan Yan, Shu-Yan Yang, Li Yang, Song Yang, Yuanming Yao, Xiaofang Yousuf, Salsabeel Yu, Hao Lei, Yu Yuan, Zhengrong Zeng, Meiyin Zhang, Chunfang Zhang, Chunge Zhang, Huimin Zhang, Jing Zhang, Na Zhang, Tianyuan Zhang, Yi-Bo Zhang, Yupeng Zhang, Zheng Zhou, Mingda Zhou, Yuanping Zhu, Chengshuai Zhu, Lin Zhu, Yue Zhu, Zhihao Zou, Hongqin Zuo, Anna Dong, Wenxuan Wen, Tao Chen, Shifu Li, Guoliang Gao, Yunyun Liu, Yong-Xin Bai, Defeng Chen, Tong Xun, Jiani Ma, Chuang Luo, Hao Yang, Haifei Cao, Chen Cao, Xiaofeng Cui, Jianzhou Deng, Yuan-Ping Deng, Zhaochao Dong, Wenxin Dong, Wenxue Du, Juan Fang, Qunkai Fang, Wei Fang, Yue Fu, Fangtian Fu, Min Fu, Yi-Tian Gao, He Ge, Jingping Gong, Qinglong Gu, Lunda Guo, Peng Guo, Yuhao Hai, Tang Liu, Hao He, Jieqiang He, Zi-Yang Hou, Huiyu Huang, Can Ji, Shuai Jiang, ChangHai Jiang, Gui-Lai Jiang, Lingjuan Jin, Ling N Kan, Yuhe Kang, Da Kou, Jin Lam, Ka-Lung Li, Changchao Li, Chong Li, Fuyi Li, Liwei Li, Miao Li, Xin Li, Ye Li, Zheng-Tao Liang, Jing Lin, Yongxin Liu, Changzhen Liu, Danni Liu, Fengqin Liu, Jia Liu, Tianrui Liu, Tingting Liu, Xinyuan Liu, Yaqun Liu, Bangyan Liu, Minghao Lou, Wenbo Luan, Yaning Luo, Yuanyuan Lv, Hujie Ma, Tengfei Mai, Zongjiong Mo, Jiayuan Niu, Dongze Pan, Zhuo Qi, Heyuan Shi, Zhanyao Song, Chunjiao Sun, Fuxiang Sun, Yan Tian, Sihui Wan, Xiulin Wang, Guoliang Wang, Hongyang Wang, Hongyu Wang, Huanhuan Wang, Jing Wang, Jun Wang, Kang Wang, Leli Wang, Shao-Kun Wang, Xinlong Wang, Yao Xiao, Zufei Xing, Huichun Xu, Yifan Yan, Shu-Yan Yang, Li Yang, Song Yang, Yuanming Yao, Xiaofang Yousuf, Salsabeel Yu, Hao Lei, Yu Yuan, Zhengrong Zeng, Meiyin Zhang, Chunfang Zhang, Chunge Zhang, Huimin Zhang, Jing Zhang, Na Zhang, Tianyuan Zhang, Yi-Bo Zhang, Yupeng Zhang, Zheng Zhou, Mingda Zhou, Yuanping Zhu, Chengshuai Zhu, Lin Zhu, Yue Zhu, Zhihao Zou, Hongqin Zuo, Anna Dong, Wenxuan Wen, Tao Chen, Shifu Li, Guoliang Gao, Yunyun Liu, Yong-Xin
collection	PubMed - marine biology
contents	EasyMetagenome: A user-friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research. Bai, Defeng Chen, Tong Xun, Jiani Ma, Chuang Luo, Hao Yang, Haifei Cao, Chen Cao, Xiaofeng Cui, Jianzhou Deng, Yuan-Ping Deng, Zhaochao Dong, Wenxin Dong, Wenxue Du, Juan Fang, Qunkai Fang, Wei Fang, Yue Fu, Fangtian Fu, Min Fu, Yi-Tian Gao, He Ge, Jingping Gong, Qinglong Gu, Lunda Guo, Peng Guo, Yuhao Hai, Tang Liu, Hao He, Jieqiang He, Zi-Yang Hou, Huiyu Huang, Can Ji, Shuai Jiang, ChangHai Jiang, Gui-Lai Jiang, Lingjuan Jin, Ling N Kan, Yuhe Kang, Da Kou, Jin Lam, Ka-Lung Li, Changchao Li, Chong Li, Fuyi Li, Liwei Li, Miao Li, Xin Li, Ye Li, Zheng-Tao Liang, Jing Lin, Yongxin Liu, Changzhen Liu, Danni Liu, Fengqin Liu, Jia Liu, Tianrui Liu, Tingting Liu, Xinyuan Liu, Yaqun Liu, Bangyan Liu, Minghao Lou, Wenbo Luan, Yaning Luo, Yuanyuan Lv, Hujie Ma, Tengfei Mai, Zongjiong Mo, Jiayuan Niu, Dongze Pan, Zhuo Qi, Heyuan Shi, Zhanyao Song, Chunjiao Sun, Fuxiang Sun, Yan Tian, Sihui Wan, Xiulin Wang, Guoliang Wang, Hongyang Wang, Hongyu Wang, Huanhuan Wang, Jing Wang, Jun Wang, Kang Wang, Leli Wang, Shao-Kun Wang, Xinlong Wang, Yao Xiao, Zufei Xing, Huichun Xu, Yifan Yan, Shu-Yan Yang, Li Yang, Song Yang, Yuanming Yao, Xiaofang Yousuf, Salsabeel Yu, Hao Lei, Yu Yuan, Zhengrong Zeng, Meiyin Zhang, Chunfang Zhang, Chunge Zhang, Huimin Zhang, Jing Zhang, Na Zhang, Tianyuan Zhang, Yi-Bo Zhang, Yupeng Zhang, Zheng Zhou, Mingda Zhou, Yuanping Zhu, Chengshuai Zhu, Lin Zhu, Yue Zhu, Zhihao Zou, Hongqin Zuo, Anna Dong, Wenxuan Wen, Tao Chen, Shifu Li, Guoliang Gao, Yunyun Liu, Yong-Xin 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.
format	Artículo científico
id	pubmed_40027489
institution	PubMed
language	en
publishDate	2025
publisher	iMeta
record_format	pubmed
spellingShingle	EasyMetagenome: A user-friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research. Bai, Defeng Chen, Tong Xun, Jiani Ma, Chuang Luo, Hao Yang, Haifei Cao, Chen Cao, Xiaofeng Cui, Jianzhou Deng, Yuan-Ping Deng, Zhaochao Dong, Wenxin Dong, Wenxue Du, Juan Fang, Qunkai Fang, Wei Fang, Yue Fu, Fangtian Fu, Min Fu, Yi-Tian Gao, He Ge, Jingping Gong, Qinglong Gu, Lunda Guo, Peng Guo, Yuhao Hai, Tang Liu, Hao He, Jieqiang He, Zi-Yang Hou, Huiyu Huang, Can Ji, Shuai Jiang, ChangHai Jiang, Gui-Lai Jiang, Lingjuan Jin, Ling N Kan, Yuhe Kang, Da Kou, Jin Lam, Ka-Lung Li, Changchao Li, Chong Li, Fuyi Li, Liwei Li, Miao Li, Xin Li, Ye Li, Zheng-Tao Liang, Jing Lin, Yongxin Liu, Changzhen Liu, Danni Liu, Fengqin Liu, Jia Liu, Tianrui Liu, Tingting Liu, Xinyuan Liu, Yaqun Liu, Bangyan Liu, Minghao Lou, Wenbo Luan, Yaning Luo, Yuanyuan Lv, Hujie Ma, Tengfei Mai, Zongjiong Mo, Jiayuan Niu, Dongze Pan, Zhuo Qi, Heyuan Shi, Zhanyao Song, Chunjiao Sun, Fuxiang Sun, Yan Tian, Sihui Wan, Xiulin Wang, Guoliang Wang, Hongyang Wang, Hongyu Wang, Huanhuan Wang, Jing Wang, Jun Wang, Kang Wang, Leli Wang, Shao-Kun Wang, Xinlong Wang, Yao Xiao, Zufei Xing, Huichun Xu, Yifan Yan, Shu-Yan Yang, Li Yang, Song Yang, Yuanming Yao, Xiaofang Yousuf, Salsabeel Yu, Hao Lei, Yu Yuan, Zhengrong Zeng, Meiyin Zhang, Chunfang Zhang, Chunge Zhang, Huimin Zhang, Jing Zhang, Na Zhang, Tianyuan Zhang, Yi-Bo Zhang, Yupeng Zhang, Zheng Zhou, Mingda Zhou, Yuanping Zhu, Chengshuai Zhu, Lin Zhu, Yue Zhu, Zhihao Zou, Hongqin Zuo, Anna Dong, Wenxuan Wen, Tao Chen, Shifu Li, Guoliang Gao, Yunyun Liu, Yong-Xin EasyMetagenome: A user-friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research. Bai, Defeng Chen, Tong Xun, Jiani Ma, Chuang Luo, Hao Yang, Haifei Cao, Chen Cao, Xiaofeng Cui, Jianzhou Deng, Yuan-Ping Deng, Zhaochao Dong, Wenxin Dong, Wenxue Du, Juan Fang, Qunkai Fang, Wei Fang, Yue Fu, Fangtian Fu, Min Fu, Yi-Tian Gao, He Ge, Jingping Gong, Qinglong Gu, Lunda Guo, Peng Guo, Yuhao Hai, Tang Liu, Hao He, Jieqiang He, Zi-Yang Hou, Huiyu Huang, Can Ji, Shuai Jiang, ChangHai Jiang, Gui-Lai Jiang, Lingjuan Jin, Ling N Kan, Yuhe Kang, Da Kou, Jin Lam, Ka-Lung Li, Changchao Li, Chong Li, Fuyi Li, Liwei Li, Miao Li, Xin Li, Ye Li, Zheng-Tao Liang, Jing Lin, Yongxin Liu, Changzhen Liu, Danni Liu, Fengqin Liu, Jia Liu, Tianrui Liu, Tingting Liu, Xinyuan Liu, Yaqun Liu, Bangyan Liu, Minghao Lou, Wenbo Luan, Yaning Luo, Yuanyuan Lv, Hujie Ma, Tengfei Mai, Zongjiong Mo, Jiayuan Niu, Dongze Pan, Zhuo Qi, Heyuan Shi, Zhanyao Song, Chunjiao Sun, Fuxiang Sun, Yan Tian, Sihui Wan, Xiulin Wang, Guoliang Wang, Hongyang Wang, Hongyu Wang, Huanhuan Wang, Jing Wang, Jun Wang, Kang Wang, Leli Wang, Shao-Kun Wang, Xinlong Wang, Yao Xiao, Zufei Xing, Huichun Xu, Yifan Yan, Shu-Yan Yang, Li Yang, Song Yang, Yuanming Yao, Xiaofang Yousuf, Salsabeel Yu, Hao Lei, Yu Yuan, Zhengrong Zeng, Meiyin Zhang, Chunfang Zhang, Chunge Zhang, Huimin Zhang, Jing Zhang, Na Zhang, Tianyuan Zhang, Yi-Bo Zhang, Yupeng Zhang, Zheng Zhou, Mingda Zhou, Yuanping Zhu, Chengshuai Zhu, Lin Zhu, Yue Zhu, Zhihao Zou, Hongqin Zuo, Anna Dong, Wenxuan Wen, Tao Chen, Shifu Li, Guoliang Gao, Yunyun Liu, Yong-Xin 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.
title	EasyMetagenome: A user-friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research.
url	https://pubmed.ncbi.nlm.nih.gov/40027489/

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