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

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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Publication Details

Journal
iMeta
Published
2025-02-01
DOI
https://doi.org/10.1002/imt2.70001
Citations
34
Primary Topic
Gut microbiota and health
Type
article
Field-Weighted Citation Impact
27.40

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article

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

Can Huang, Jiayuan Mo, Shifu Chen, Xinlong Wang et al.
34 citations
iMeta
Gut microbiota and health
27.40
article

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

Can Huang, Jiayuan Mo, Shifu Chen, Xinlong Wang, Chengshuai Zhu, Yao Wang, Tong Chen, Wenxue Dong, Zhengrong Yuan, Yuanming Yang, Tao Wen, Chunjiao Song, Lin Zhu, Leli Wang, Zhuo Pan, Jianzhou Cui, Yifan Xu, Fang Wei, Zong-Jiong Mai, Ka‐Lung Lam, Ling Jin, Anna Zuo, Hongyu Wang, Kou Jin, Weimin Dong, Dongze Niu, Li Yang, Jieqiang He, Yongxin Lin, Tianrui Liu, Fangcheng Fu, Tengfei Ma, Sun Fu-xiang, Zhaochao Deng, Qunkai Fang, Juan Du, Xiulin Wan, Bangyan Liu, Defeng Bai, Lingjuan Jiang, Heyuan Qi, Jingping Ge, Yuhao Guo, Shuo Wang, Jia Liu, Chunge Zhang, Yunyun Gao, Yupeng Zhang, Yuhe Kan, Yaning Luan, Xiaofeng Cao, Changchao Li, Fuyi Li, Xinyuan Zhang, Guilai Jiang, Mingda Zhou, Yaqun Liu, Honghao Lv, Yuanyuan Luo, Salsabeel Yousuf, Wenbo Lou, C.-S. Jiang, Huichun Xing, Yuanping Zhou, Lunda Gu, Song Yang, Da Kang, Hao Yu, Ye Li, Jing Zhang, Xin Li, Jing Wang, Huimin Zhang, Kang Wang, Jun Wang, Na Zhang, Chong Li, Tingting Liu, Ming Zeng, Yibo Zhang, Guoliang Li, Hao Liu, Xiaofang Yao, Liwei Li, Chen Cao, Guo‐Liang Wang, Xin‐Yuan Liu, Jing Liang, Minghao Liu, Miao Li, Hongyang Wang, Yongxin Liu, Tianyuan Zhang, Chunfang Zhang, Min Fu, He Gao, Sihui Tian, Yue Fang, Changzhen Liu, Zhengtao Li, Shu Yan, Danni Liu, Zufei Xiao, Fengqin Liu, Wenxuan Dong, Yuan‐Ping Deng, Hongqin Zou, Qing-Long Gong, Jiani Xun, Shuai Ji, Zhihao Zhu, Zhanyao Shi, Hao Luo, Yue Zhu, Huanhuan Wang, Tang Hai, Yan Sun, Yingxun Fu, Yu Lei, Peng Guo, Chuang Ma, Huiyu Hou, Haifei Yang, Zi‐Yang He
article en
34 citations

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.

iMetaVol. 4(1)
Shihezi University (CN), Hebei University of Engineering (CN), Jiangxi University of Traditional Chinese Medicine (CN), Fujian Normal University (CN), Beijing Union University (CN), Tongji University (CN), Guangzhou University of Chinese Medicine (CN), Nanjing Agricultural University (CN), Zhejiang A & F University (CN), University of Helsinki (FI), Guangdong University of Technology (CN), Central South University (CN), Anhui Agricultural University (CN), Hong Kong Polytechnic University (HK), Qingdao Agricultural University (CN), Guangxi University (CN), University of Alberta (CA), Sun Yat-sen University (CN), Guangxi Medical University (CN), Xizang Minzu University (CN), The University of Melbourne (AU), National University of Singapore (SG), Guangdong Medical College (CN), Chinese University of Hong Kong (HK), Capital Medical University (CN), Chinese Center For Disease Control and Prevention (CN), Anhui University of Science and Technology (CN), Northeast Normal University (CN), Chinese Academy of Sciences (CN), Chinese Academy of Medical Sciences & Peking Union Medical College (CN), Harbin Institute of Technology (CN), Nankai University (CN), Purdue University West Lafayette (US), Beijing Normal University (CN), University of Michigan (US), Peking Union Medical College Hospital (CN), Karolinska Institutet (SE), Lanzhou Jiaotong University (CN), Beijing Forestry University (CN), Zhejiang Ocean University (CN), Hebei University of Science and Technology (CN), Beijing University of Technology (CN), Zhengzhou University (CN), Soochow University (CN), Shenzhen Bioeasy Biotechnology (China) (CN), Agricultural Genomics Institute at Shenzhen (CN), Institute of Plant Protection (CN), Guangdong Academy of Sciences (CN), Institute of Subtropical Agriculture (CN), Institute of Agricultural Resources and Regional Planning (CN), Anhui Science and Technology University (CN), Fifth Affiliated Hospital of Sun Yat-sen University (CN), Gannan Medical University (CN), Deyang Stomatological Hospital (CN), Institute of Urban Environment (CN), Microbiology Institute of Shaanxi (CN), State Key Joint Laboratory of Environment Simulation and Pollution Control (CN), Chinese Academy of Forestry (CN), Agro-Environmental Protection Institute (CN), Institute of Microbiology (CN), Chinese Academy of Agricultural Sciences (CN), China Academy of Chinese Medical Sciences (CN), Hangzhou DAC Biotech (China) (CN), Beijing Academy of Agricultural and Forestry Sciences (CN), Tea Research Institute (CN), Beijing Ditan Hospital (CN), Sansure Biotech (China) (CN), Ministry of Agriculture and Rural Affairs (CN), Jilin Agricultural University (CN), Changzhou University (CN), Chinese Research Academy of Environmental Sciences (CN), Institute of Botany (CN), Institute of Soil Science (CN), Hanshan Normal University (CN), Ecosystem Sciences (AU), Henan Agricultural University (CN), Imperial College London (GB), Hunan Agricultural University (CN), Shanxi Datong University (CN), Heilongjiang University (CN), Zhejiang University of Technology (CN), Southern Medical University (CN), City University of Macau (MO), Weifang University (CN), Xi’an Jiaotong-Liverpool University (CN), The University of Tokyo (JP), Jiangxi Agricultural University (CN), Zhejiang University (CN), Lanzhou University (CN), Yangzhou University (CN), Nanjing Medical University (CN), Northwest A&F University (CN), Shanghai Maritime University (CN), Tsinghua University (CN)
National Natural Science Foundation of China, China Postdoctoral Science Foundation, Agricultural Science and Technology Innovation Program
Industry, innovation and infrastructure
Openalex Percentile: Top 0%
Gut microbiota and health
27.40
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