Publication Details

Category Text Publication
Reference Category Journals
DOI 10.1111/1755-0998.13904
Licence creative commons licence
Title (Primary) MuDoGeR: Multi-Domain Genome recovery from metagenomes made easy
Author Nunes da Rocha, U.; Kasmanas, J.C.; Kallies, R.; Saraiva, J.P.; Brizola Toscan, R.; Štefanič, P.; Fleming Bicalho, M.; Borim Correa, F.; Baştürk, M.N.; Fousekis, E.; Viana Barbosa, L.M.; Plewka, J.; Probst, A.J.; Baldrian, P.; Stadler, P.F.; CLUE-TERRA consortium,
Source Titel Molecular Ecology Resources
Year 2024
Department AME
Volume 24
Issue 2
Page From e13904
Language englisch
Topic T7 Bioeconomy
Keywords genome reconstruction; metagenome-assembled genomes; metagenomics; multi-domain; uncultivated viral genomes
Abstract 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 Additionally, MuDoGeR is also available as a Singularity container. 
Persistent UFZ Identifier
Nunes da Rocha, U., Kasmanas, J.C., Kallies, R., Saraiva, J.P., Brizola Toscan, R., Štefanič, P., Fleming Bicalho, M., Borim Correa, F., Baştürk, M.N., Fousekis, E., Viana Barbosa, L.M., Plewka, J., Probst, A.J., Baldrian, P., Stadler, P.F., CLUE-TERRA consortium, (2024):
MuDoGeR: Multi-Domain Genome recovery from metagenomes made easy
Mol. Ecol. Resour. 24 (2), e13904 10.1111/1755-0998.13904