Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ONT N2L 3G1, Canada.
Gigascience. 2021 Feb 3;10(2). doi: 10.1093/gigascience/giab006.
Advances in high-throughput sequencing accessibility have democratized small subunit ribosomal RNA gene sequence data collection, coincident with an increasing availability of computational tools for sequence data processing, multivariate statistics, and data visualization. However, existing tools often require programming ability and frequent user intervention that may not be suitable for fast-paced and large-scale data analysis by end user microbiologists who are unfamiliar with the Linux command line environment or who prefer interactions with a GUI. Here we present AXIOME3, which is a completely redeveloped AXIOME pipeline that streamlines small subunit ribosomal RNA data analysis by managing QIIME2, R, and Python-associated analyses through an interactive web interface.
AXIOME3 comes with web GUI to improve usability by simplifying configuration processes and task status tracking. Internally, it uses an automated pipeline that is wrapped around QIIME2 to generate a range of outputs including amplicon sequence variant tables, taxonomic classifications, phylogenetic trees, biodiversity metrics, and ordinations. The extension module for AXIOME3 provides advanced data visualization tools such as principal coordinate analysis, bubble plots, and triplot ordinations that can be used to visualize interactions between a distance matrix, amplicon sequence variant taxonomy, and sample metadata.
Because repeat analysis of small subunit ribosomal RNA amplicon sequence data is challenging for those who have limited experience in command line environments, AXIOME3 now offers rapid and user-friendly options within an automated pipeline, with advanced data visualization tools and the ability for users to incorporate additional analyses easily through extension. AXIOME3 is completely open source (https://github.com/neufeld/AXIOME3, https://github.com/neufeld/AXIOME3-GUI), and researchers are encouraged to modify and redistribute the package.
高通量测序技术的进步使小亚基核糖体 RNA 基因序列数据的收集民主化，同时也为序列数据处理、多元统计和数据可视化的计算工具提供了更多的可用性。然而，现有的工具通常需要编程能力和频繁的用户干预，这可能不适合不熟悉 Linux 命令行环境或更喜欢使用图形用户界面交互的终端用户微生物学家进行快速和大规模数据分析。在这里，我们提出了 AXIOME3，这是一个完全重新开发的 AXIOME 管道，通过通过交互式 Web 界面管理 QIIME2、R 和 Python 相关分析，简化了小亚基核糖体 RNA 数据分析。
AXIOME3 带有 Web GUI，通过简化配置过程和任务状态跟踪来提高可用性。在内部，它使用一个自动化管道，该管道围绕 QIIME2 进行包装，生成一系列输出，包括扩增子序列变异表、分类学分类、系统发育树、生物多样性指标和排序。AXIOME3 的扩展模块提供了高级数据可视化工具，如主坐标分析、气泡图和三角图排序，可以用于可视化距离矩阵、扩增子序列变异分类学和样本元数据之间的相互作用。
由于对于那些在命令行环境中经验有限的人来说，重复分析小亚基核糖体 RNA 扩增子序列数据具有挑战性，因此 AXIOME3 现在在自动化管道中提供了快速和用户友好的选项，具有高级数据可视化工具和用户通过扩展轻松纳入其他分析的能力。AXIOME3 是完全开源的（https://github.com/neufeld/AXIOME3，https://github.com/neufeld/AXIOME3-GUI），鼓励研究人员修改和重新分发该软件包。
