BusyBee Web: towards comprehensive and differential composition-based metagenomic binning

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. [GRAPHICS] .

Automated summary

Despite improvements in taxonomic profiling tools, metagenomic assembly and genomic binning remain important in metagenomic analysis workflows. The tool BusyBee Web implements a composition-based binning method, capable of handling both assembled contigs and nanopore generated reads. It now offers comprehensive visualizations, allows for differential analysis of samples, and offers plasmid sequence checking using PLSDB as a reference database. Additionally, it provides an API and a Python package for automated access.