Several computational frameworks and workflows that recover genomes from prokaryotes, eukaryotes and viruses from metagenomes exist. Yet, it is difficult for scientists with little bioinformatics experience to evaluate quality, annotate genes, dereplicate, assign taxonomy and calculate relative abundance and coverage of genomes belonging to different domains. MuDoGeR is a user-friendly tool tailored for those familiar with Unix command-line environment that makes it easy to recover genomes of prokaryotes, eukaryotes and viruses from metagenomes, either alone or in combination. We tested MuDoGeR using 24 individual-isolated genomes and 574 metagenomes, demonstrating the applicability for a few samples and high throughput. While MuDoGeR can recover eukaryotic viral sequences, its characterization is predominantly skewed towards bacterial and archaeal viruses, reflecting the field's current state. However, acting as a dynamic wrapper, the MuDoGeR is designed to constantly incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field. MuDoGeR is open-source software available at https://github.com/mdsufz/MuDoGeR. Additionally, MuDoGeR is also available as a Singularity container.

Biotechnical Faculty University of Ljubljana Ljubljana Slovenia

Department of Computer Science and Interdisciplinary Center of Bioinformatics University of Leipzig Leipzig Germany

Department of Environmental Microbiology Helmholtz Centre for Environmental Research UFZ Leipzig Germany

Environmental Microbiology and Biotechnology Department of Chemistry University of Duisburg Essen Essen Germany

Institute for Theoretical Chemistry University of Vienna Vienna Austria

Institute of Mathematics and Computer Sciences University of São Paulo São Carlos Brazil

Laboratory of Environmental Microbiology Institute of Microbiology of the Czech Academy of Sciences Praha 4 Czech Republic

Max Planck Institute for Mathematics in the Sciences Leipzig Germany

The Santa Fe Institute Santa Fe New Mexico USA

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