Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.
Clinical Bioinformatics (CLIB), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany.
Nucleic Acids Res. 2022 Jul 5;50(W1):W132-W137. doi: 10.1093/nar/gkac298.
Despite recent methodology and reference database improvements for taxonomic profiling tools, metagenomic assembly and genomic binning remain important pillars of metagenomic analysis workflows. In case reference information is lacking, genomic binning is considered to be a state-of-the-art method in mixed culture metagenomic data analysis. In this light, our previously published tool BusyBee Web implements a composition-based binning method efficient enough to function as a rapid online utility. Handling assembled contigs and long nanopore generated reads alike, the webserver provides a wide range of supplementary annotations and visualizations. Half a decade after the initial publication, we revisited existing functionality, added comprehensive visualizations, and increased the number of data analysis customization options for further experimentation. The webserver now allows for visualization-supported differential analysis of samples, which is computationally expensive and typically only performed in coverage-based binning methods. Further, users may now optionally check their uploaded samples for plasmid sequences using PLSDB as a reference database. Lastly, a new application programming interface with a supporting python package was implemented, to allow power users fully automated access to the resource and integration into existing workflows. The webserver is freely available under: https://www.ccb.uni-saarland.de/busybee.
尽管分类学分析工具的方法和参考数据库最近有所改进，但宏基因组组装和基因组分箱仍然是宏基因组分析工作流程的重要支柱。如果缺乏参考信息，基因组分箱被认为是混合培养宏基因组数据分析的一种最新方法。有鉴于此，我们之前发布的工具 BusyBee Web 实现了一种基于组成的分箱方法，其效率足以用作快速在线实用程序。该网络服务器可以处理组装的连续序列和长纳米孔生成的读取，提供广泛的补充注释和可视化。在最初发布五年后，我们重新审视了现有的功能，添加了全面的可视化，并增加了数据分析定制选项的数量，以进行进一步的实验。该网络服务器现在允许对样本进行支持可视化的差异分析，这在计算上很昂贵，通常仅在基于覆盖度的分箱方法中进行。此外，用户现在可以选择使用 PLSDB 作为参考数据库来检查其上传样本中的质粒序列。最后，实现了一个带有支持的 Python 包的新应用程序编程接口，允许高级用户完全自动化访问资源并集成到现有工作流程中。该网络服务器可在以下网址免费获得：https://www.ccb.uni-saarland.de/busybee。
