Liu Yong-Xin, Chen Lei, Ma Tengfei, Li Xiaofang, Zheng Maosheng, Zhou Xin, Chen Liang, Qian Xubo, Xi Jiao, Lu Hongye, Cao Huiluo, Ma Xiaoya, Bian Bian, Zhang Pengfan, Wu Jiqiu, Gan Ren-You, Jia Baolei, Sun Linyang, Ju Zhicheng, Gao Yunyun, Wen Tao, Chen Tong
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen Guangdong China.
Department of Vascular Surgery, Fu Xing Hospital Capital Medical University Beijing China.
Imeta. 2023 Jan 27;2(1):e83. doi: 10.1002/imt2.83. eCollection 2023 Feb.
It is difficult for beginners to learn and use amplicon analysis software because there are so many software tools to choose from, and all of them need multiple steps of operation. Herein, we provide a cross-platform, open-source, and community-supported analysis pipeline EasyAmplicon. EasyAmplicon has most of the modules needed for an amplicon analysis, including data quality control, merging of paired-end reads, dereplication, clustering or denoising, chimera detection, generation of feature tables, taxonomic diversity analysis, compositional analysis, biomarker discovery, and publication-quality visualization. EasyAmplicon includes more than 30 cross-platform modules and R packages commonly used in the field. All steps of the pipeline are integrated into RStudio, which reduces learning costs, keeps the flexibility of the analysis process, and facilitates personalized analysis. The pipeline is maintained and updated by the authors and editors of WeChat official account "Meta-genome." Our team will regularly release the latest tutorials both in Chinese and English, read the feedback from users, and provide help to them in the WeChat account and GitHub. The pipeline can be deployed on various platforms, and the installation time is less than half an hour. On an ordinary laptop, the whole analysis process for dozens of samples can be completed within 3 h. The pipeline is available at GitHub (https://github.com/YongxinLiu/EasyAmplicon) and Gitee (https://gitee.com/YongxinLiu/EasyAmplicon).
对于初学者来说，学习和使用扩增子分析软件很困难，因为可供选择的软件工具太多，而且所有这些工具都需要多个操作步骤。在此，我们提供了一个跨平台、开源且由社区支持的分析流程EasyAmplicon。EasyAmplicon具备扩增子分析所需的大部分模块，包括数据质量控制、双端读段合并、去重、聚类或降噪、嵌合体检测、特征表生成、分类多样性分析、成分分析、生物标志物发现以及高质量的可视化展示。EasyAmplicon包含30多个该领域常用的跨平台模块和R包。该流程的所有步骤都集成到了RStudio中，这降低了学习成本，保持了分析过程的灵活性，并便于进行个性化分析。该流程由微信公众号“宏基因组”的作者和编辑维护与更新。我们的团队将定期发布中英文最新教程，阅读用户反馈，并在微信公众号和GitHub上为他们提供帮助。该流程可以部署在各种平台上，安装时间不到半小时。在普通笔记本电脑上，数十个样本的整个分析过程可以在3小时内完成。该流程可在GitHub（https://github.com/YongxinLiu/EasyAmplicon）和Gitee（https://gitee.com/YongxinLiu/EasyAmplicon）上获取。
