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

doi:10.1002/imt2.70001

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 FuHe 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

School of Science

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Pages (from-to)	e70001
Journal	iMeta
Volume	4
Issue number	1
DOIs	https://doi.org/10.1002/imt2.70001
Publication status	Published - 2025

Keywords

metagenome microbiome microbiota pipeline visualization

Access to Document

10.1002/imt2.70001

https://onlinelibrary.wiley.com/doi/abs/10.1002/imt2.70001

Cite this

@article{7b44271a07704b04a9c8846de39cc1fb,

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

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 = "metagenome microbiome microbiota pipeline visualization",

author = "Defeng Bai and Tong Chen and Jiani Xun and Chuang Ma and Hao Luo and Haifei Yang and Chen Cao and Xiaofeng Cao and Jianzhou Cui and Yuan-Ping Deng and Zhaochao Deng and Wenxin Dong and Wenxue Dong and Juan Du and Qunkai Fang and Wei Fang and Yue Fang and Fangtian Fu and Min Fu and Yi-Tian Fu and He Gao and Jingping Ge and Qinglong Gong and Lunda Gu and Peng Guo and Yuhao Guo and Tang Hai and Hao Liu and Jieqiang He and Zi-Yang He and Huiyu Hou and Can Huang and Shuai Ji and ChangHai Jiang and Gui-Lai Jiang and Lingjuan Jiang and Jin, \{Ling N.\} and Yuhe Kan and Da Kang and Jin Kou and Ka-Lung Lam and Changchao Li and Chong Li and Fuyi Li and Liwei Li and Miao Li and Xin Li and Ye Li and Zheng-Tao Li and Jing Liang and Yongxin Lin and Changzhen Liu and Danni Liu and Fengqin Liu and Jia Liu and Tianrui Liu and Tingting Liu and Xinyuan Liu and Yaqun Liu and Bangyan Liu and Minghao Liu and Wenbo Lou and Yaning Luan and Yuanyuan Luo and Hujie Lv and Tengfei Ma and Zongjiong Mai and Jiayuan Mo and Dongze Niu and Zhuo Pan and Heyuan Qi and Zhanyao Shi and Chunjiao Song and Fuxiang Sun and Yan Sun and Sihui Tian and Xiulin Wan and Guoliang Wang and Hongyang Wang and Hongyu Wang and Huanhuan Wang and Jing Wang and Jun Wang and Kang Wang and Leli Wang and Shao-kun Wang and Xinlong Wang and Yao Wang and Zufei Xiao and Huichun Xing and Yifan Xu and Shu-yan Yan and Li Yang and Song Yang and Yuanming Yang and Xiaofang Yao and Salsabeel Yousuf and Hao Yu and Yu Lei and Zhengrong Yuan and Meiyin Zeng and Chunfang Zhang and Chunge Zhang and Huimin Zhang and Jing Zhang and Na Zhang and Tianyuan Zhang and Yi-Bo Zhang and Yupeng Zhang and Zheng Zhang and Mingda Zhou and Yuanping Zhou and Chengshuai Zhu and Lin Zhu and Yue Zhu and Zhihao Zhu and Hongqin Zou and Anna Zuo and Wenxuan Dong and Tao Wen and Shifu Chen and Guoliang Li and Yunyun Gao and Yong-Xin Liu",

year = "2025",

doi = "10.1002/imt2.70001",

language = "English",

volume = "4",

pages = "e70001",

journal = "iMeta",

issn = "2770-5986",

number = "1",

}

Bai, D, Chen, T, Xun, J, Ma, C, Luo, H, Yang, H, Cao, C, Cao, X, Cui, J, Deng, Y-P, Deng, Z, Dong, W, Dong, W, Du, J, Fang, Q, Fang, W, Fang, Y, Fu, F, Fu, M, Fu, Y-T, Gao, H, Ge, J, Gong, Q, Gu, L, Guo, P, Guo, Y, Hai, T, Liu, H, He, J, He, Z-Y, Hou, H, Huang, C, Ji, S, Jiang, C, Jiang, G-L, Jiang, L, Jin, LN, Kan, Y, Kang, D, Kou, J, Lam, K-L, Li, C, Li, C, Li, F, Li, L, Li, M, Li, X, Li, Y, Li, Z-T, Liang, J, Lin, Y, Liu, C, Liu, D, Liu, F, Liu, J, Liu, T, Liu, T, Liu, X, Liu, Y, Liu, B, Liu, M, Lou, W, Luan, Y, Luo, Y, Lv, H, Ma, T, Mai, Z, Mo, J, Niu, D, Pan, Z, Qi, H, Shi, Z, Song, C, Sun, F, Sun, Y, Tian, S, Wan, X, Wang, G, Wang, H, Wang, H, Wang, H, Wang, J, Wang, J, Wang, K, Wang, L, Wang, S, Wang, X, Wang, Y, Xiao, Z, Xing, H, Xu, Y, Yan, S, Yang, L, Yang, S, Yang, Y, Yao, X, Yousuf, S, Yu, H, Lei, Y, Yuan, Z, Zeng, M, Zhang, C, Zhang, C, Zhang, H, Zhang, J, Zhang, N, Zhang, T, Zhang, Y-B, Zhang, Y, Zhang, Z, Zhou, M, Zhou, Y, Zhu, C, Zhu, L, Zhu, Y, Zhu, Z, Zou, H, Zuo, A, Dong, W, Wen, T, Chen, S, Li, G, Gao, Y & Liu, Y-X 2025, 'EasyMetagenome: A user-friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research', iMeta, vol. 4, no. 1, pp. e70001. https://doi.org/10.1002/imt2.70001

TY - JOUR

T1 - EasyMetagenome: A user-friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research

AU - Bai, Defeng

AU - Chen, Tong

AU - Xun, Jiani

AU - Ma, Chuang

AU - Luo, Hao

AU - Yang, Haifei

AU - Cao, Chen

AU - Cao, Xiaofeng

AU - Cui, Jianzhou

AU - Deng, Yuan-Ping

AU - Deng, Zhaochao

AU - Dong, Wenxin

AU - Dong, Wenxue

AU - Du, Juan

AU - Fang, Qunkai

AU - Fang, Wei

AU - Fang, Yue

AU - Fu, Fangtian

AU - Fu, Min

AU - Fu, Yi-Tian

AU - Gao, He

AU - Ge, Jingping

AU - Gong, Qinglong

AU - Gu, Lunda

AU - Guo, Peng

AU - Guo, Yuhao

AU - Hai, Tang

AU - Liu, Hao

AU - He, Jieqiang

AU - He, Zi-Yang

AU - Hou, Huiyu

AU - Huang, Can

AU - Ji, Shuai

AU - Jiang, ChangHai

AU - Jiang, Gui-Lai

AU - Jiang, Lingjuan

AU - Jin, Ling N.

AU - Kan, Yuhe

AU - Kang, Da

AU - Kou, Jin

AU - Lam, Ka-Lung

AU - Li, Changchao

AU - Li, Chong

AU - Li, Fuyi

AU - Li, Liwei

AU - Li, Miao

AU - Li, Xin

AU - Li, Ye

AU - Li, Zheng-Tao

AU - Liang, Jing

AU - Lin, Yongxin

AU - Liu, Changzhen

AU - Liu, Danni

AU - Liu, Fengqin

AU - Liu, Jia

AU - Liu, Tianrui

AU - Liu, Tingting

AU - Liu, Xinyuan

AU - Liu, Yaqun

AU - Liu, Bangyan

AU - Liu, Minghao

AU - Lou, Wenbo

AU - Luan, Yaning

AU - Luo, Yuanyuan

AU - Lv, Hujie

AU - Ma, Tengfei

AU - Mai, Zongjiong

AU - Mo, Jiayuan

AU - Niu, Dongze

AU - Pan, Zhuo

AU - Qi, Heyuan

AU - Shi, Zhanyao

AU - Song, Chunjiao

AU - Sun, Fuxiang

AU - Sun, Yan

AU - Tian, Sihui

AU - Wan, Xiulin

AU - Wang, Guoliang

AU - Wang, Hongyang

AU - Wang, Hongyu

AU - Wang, Huanhuan

AU - Wang, Jing

AU - Wang, Jun

AU - Wang, Kang

AU - Wang, Leli

AU - Wang, Shao-kun

AU - Wang, Xinlong

AU - Wang, Yao

AU - Xiao, Zufei

AU - Xing, Huichun

AU - Xu, Yifan

AU - Yan, Shu-yan

AU - Yang, Li

AU - Yang, Song

AU - Yang, Yuanming

AU - Yao, Xiaofang

AU - Yousuf, Salsabeel

AU - Yu, Hao

AU - Lei, Yu

AU - Yuan, Zhengrong

AU - Zeng, Meiyin

AU - Zhang, Chunfang

AU - Zhang, Chunge

AU - Zhang, Huimin

AU - Zhang, Jing

AU - Zhang, Na

AU - Zhang, Tianyuan

AU - Zhang, Yi-Bo

AU - Zhang, Yupeng

AU - Zhang, Zheng

AU - Zhou, Mingda

AU - Zhou, Yuanping

AU - Zhu, Chengshuai

AU - Zhu, Lin

AU - Zhu, Yue

AU - Zhu, Zhihao

AU - Zou, Hongqin

AU - Zuo, Anna

AU - Dong, Wenxuan

AU - Wen, Tao

AU - Chen, Shifu

AU - Li, Guoliang

AU - Gao, Yunyun

AU - Liu, Yong-Xin

PY - 2025

Y1 - 2025

N2 - 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.

AB - 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.

KW - metagenome microbiome microbiota pipeline visualization

U2 - 10.1002/imt2.70001

DO - 10.1002/imt2.70001

M3 - Article

SN - 2770-5986

VL - 4

SP - e70001

JO - iMeta

JF - iMeta

IS - 1

ER -

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

Abstract

Keywords

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