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iMeta · 2025

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

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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

Аннотация

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.

ИП Урсолов Владлен Сергеевич

ИНН 500118482352 · ОГРНИП 314500117700049

Реквизиты и контакты