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, Weimin Dong, Wenxue Dong, Juan Du, Qunkai Fang, Fang Wei, Yue Fang, Fangcheng Fu, Min Fu, Yingxun Fu, He Gao, Jingping Ge, Qing-Long Gong, Lunda Gu, Peng Guo, Yuhao Guo, Tang Hai, Hao Liu, Jieqiang He, Zi‐Yang He, Huiyu Hou, Can Huang, Shuai Ji, ChangHai Jiang, Guilai Jiang, Lingjuan Jiang, Ling Jin, Yuhe Kan, Da Kang, Kou Jin, Ka‐Lung Lam, Changchao Li, Chong Li, Fuyi Li, Liwei Li, Miao Li, Xin Li, Ye Li, Zhengtao Li, Jing Liang, Yongxin Lin, Changzhen Liu, Danni Liu, Fengqin Liu, Jia Liu, Tianrui Liu, Tingting Liu, Xin‐Yuan Liu, Yaqun Liu, Bangyan Liu, Minghao Liu, Wenbo Lou, Yaning Luan, Yuanyuan Luo, Honghao Lv, Tengfei Ma, Zong-Jiong Mai, Jiayuan Mo, Dongze Niu, Zhuo Pan, Heyuan Qi, Zhanyao Shi, Chunjiao Song, Chunjiao Song, Yan Sun, Sihui Tian, Xiulin Wan, Guo‐Liang Wang, Guoliang Wang, Hongyu Wang, Huanhuan Wang, Jing Wang, Jun Wang, Kang Wang, Leli Wang, Leli Wang, Xinlong Wang, Yao Wang, Zufei Xiao, Huichun Xing, Yifan Xu, Shu Yan, Li Yang, Song Yang, Yuanming Yang, Xiaofang Yao, Salsabeel Yousuf, Hao Yu, Yu Lei, Zhengrong Yuan
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.