The Metagenomics-Toolkit - A new workflow pearl available on the Cloud based Workflow Manager (CloWM)

With the Metagenomics-Toolkit (Belmann, Osterholz et al. 2024) a new scalable workflow for the analysis of metagenomic data is now available on the CloWM platform (https://clowm.bi.denbi.de). The data agnostic workflow supports processing of short and long reads and allows for a full end-to-end metagenomics analysis. Beside the standard analysis steps, quality control, assembly, binning and annotation the workflow has several distinctive features, such as

• plasmid identification based on various tools,
• recovery of unassembled microbial community members,
• discovery of microbial interdependencies through a combination of dereplication, co-occurrence, and genome-scale metabolic modeling.

The Metagenomics-Toolkit workflow is open source, and freely available on the CloWM platform.