简易宏基因组：微生物组研究中用于鸟枪法宏基因组分析的用户友好型灵活流程。
EasyMetagenome: A user-friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research.
作者信息
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
机构信息
Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China.
State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing China.
出版信息
Imeta. 2025 Feb 14;4(1):e70001. doi: 10.1002/imt2.70001. eCollection 2025 Feb.
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.
鸟枪法宏基因组学已成为微生物组研究中的一项关键技术，能够在高分辨率分类学和功能水平上对微生物群落进行深入分析。这种方法为微生物多样性、相互作用及其在健康和疾病中的作用提供了有价值的见解。然而，数据处理的复杂性和可重复性的需求给研究人员带来了重大挑战。为应对这些挑战，我们开发了EasyMetagenome，这是一个用户友好的流程，支持多种分析方法，包括质量控制和宿主去除、基于 reads 的分析、基于组装的分析和分箱，以及先进的基因组分析。该流程还具有可定制的设置、全面的数据可视化和详细的参数解释，确保其在广泛的数据场景中具有适应性。展望未来，我们旨在通过解决宿主污染问题、优化第三代测序数据的工作流程以及整合深度学习和网络分析等新兴技术来完善该流程，以进一步增强对微生物组的见解和数据准确性。EasyMetageonome可在https://github.com/YongxinLiu/EasyMetagenome上免费获取。
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