ELIXIR FAIRyMAGs

Metagenomics Assembled Genomes (MAGs) are crucial for understanding biodiversity, enhancing food security and combating pathogens by providing insight on uncultured and unexplored genomes. The FAIRyMAGs project, funded as a CoS by ELIXIR, aims at advancing metagenomics research through the advancement, optimisation, evaluation and dissemination of robust FAIR workflows for building MAGs. It is co-led by Bérénice Batut and Paul Zierep (Uni. of Freiburg, Germany), and involves Martin Beracochea (EMBL-EBI), Bruno Fosso (Uni. of Bari, Italy), Giuseppe Defasazio (Uni. of Bari, Italy), and Mina Ansari (Uni. of Freiburg, Germany).

Leveraging the Galaxy platform, our primary objectives include finalising a user-friendly state-of-the-art Galaxy workflow tailored for MAG construction, and ensuring its accessibility and reusability through integration with WorkflowHub. To support user adoption and proficiency, we will create FAIR educational materials hosted on the Galaxy Training Network (GTN), empowering researchers with the skills necessary to use the workflow effectively.

The efficacy of the developed workflow will be rigorously evaluated by analysing MAGs generated from simulated and real-world data-spanning diverse environments: atmosphere, marine and cow gut microbiomes. This evaluation will provide valuable insights into the workflow’s performance and its applicability across different sample types, complexities and ecosystems.

We will also investigate the computational resources required for executing the assembly step of the workflow using data provided by several Galaxy servers and the MGnify team on various input datasets. The aim would be to optimise resource allocation to ensure efficient and cost-effective MAGs construction. A novel tool will be developed to facilitate this process, allowing researchers to accurately estimate and allocate resources for each step of the assembly pipeline.

By addressing these objectives, our project aims to accelerate metagenomics research by providing researchers with a comprehensive and accessible framework for MAGs construction. This framework will not only streamline the workflow for building MAGs but also facilitate reproducibility, collaboration and innovation within the ELIXIR Microbiome Community.