EasyMetagenome:一个用户友好且灵活的管道,用于微生物组研究中的霰弹枪宏基因组分析

IF 23.7 Q1 MICROBIOLOGY
iMeta Pub Date : 2025-02-14 DOI:10.1002/imt2.70001
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
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引用次数: 0

摘要

霰弹枪宏基因组学已经成为微生物组研究的关键技术,可以在高分辨率的分类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对可重复性的需求给研究人员带来了重大挑战。为了应对这些挑战,我们开发了EasyMetagenome,这是一个用户友好的管道,支持多种分析方法,包括质量控制和宿主去除,基于读取,基于装配和分组,以及先进的基因组分析。该管道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的适应性。展望未来,我们的目标是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管道,以进一步提高微生物组的洞察力和数据准确性。EasyMetageonome可在https://github.com/YongxinLiu/EasyMetagenome免费获得。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

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

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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