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MuDoGeR: Multi‐Domain Genome recovery from metagenomes made easy

Rocha, Ulisses ; Coelho Kasmanas, Jonas ; Kallies, René ; Saraiva, Joao Pedro ; Toscan, Rodolfo Brizola ; Štefanič, Polonca ; Bicalho, Marcos Fleming ; Borim Correa, Felipe ; Baştürk, Merve Nida ; Fousekis, Efthymios ; Viana Barbosa, Luiz Miguel ; Plewka, Julia ; Probst, Alexander J. ; Baldrian, Petr ; Stadler, Peter F. ; Bartholomäus, Alexander ; Rosado, Alexandre Soares ; Fiore‐Donno, Ana‐Maria ; Leon Ferreira de Carvalho, André Carlos Ponce ; Gubry‐Rangin, Cecile ; Machado, Daniel ; Sanches, Danilo S. ; Wagner, Dirk ; Berg, Gabriele ; Mulec, Ines Mundic ; Muehe, Marie ; Bonkowski, Michael ; Gomes, Newton ; Peixoto, Raquel ; Costa, Rodrigo ; Kleinsteuber, Sabine ; Gribaldo, Simonetta ; Costa, Tina Keller ; Pellizari, Vivian

Molecular ecology resources, 2024-02, Vol.24 (2), p.e13904-n/a [Periódico revisado por pares]

England: Wiley Subscription Services, Inc

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Título:
MuDoGeR: Multi‐Domain Genome recovery from metagenomes made easy
Autor: Rocha, Ulisses ; Coelho Kasmanas, Jonas ; Kallies, René ; Saraiva, Joao Pedro ; Toscan, Rodolfo Brizola ; Štefanič, Polonca ; Bicalho, Marcos Fleming ; Borim Correa, Felipe ; Baştürk, Merve Nida ; Fousekis, Efthymios ; Viana Barbosa, Luiz Miguel ; Plewka, Julia ; Probst, Alexander J. ; Baldrian, Petr ; Stadler, Peter F. ; Bartholomäus, Alexander ; Rosado, Alexandre Soares ; Fiore‐Donno, Ana‐Maria ; Leon Ferreira de Carvalho, André Carlos Ponce ; Gubry‐Rangin, Cecile ; Machado, Daniel ; Sanches, Danilo S. ; Wagner, Dirk ; Berg, Gabriele ; Mulec, Ines Mundic ; Muehe, Marie ; Bonkowski, Michael ; Gomes, Newton ; Peixoto, Raquel ; Costa, Rodrigo ; Kleinsteuber, Sabine ; Gribaldo, Simonetta ; Costa, Tina Keller ; Pellizari, Vivian
Assuntos: Bacteria - genetics ; Bioinformatics ; Eukaryotes ; genome reconstruction ; Genomes ; Metagenome ; metagenome‐assembled genomes ; Metagenomics ; multi‐domain ; Phylogeny ; Prokaryotes ; Relative abundance ; Software ; Taxonomy ; uncultivated viral genomes ; Viruses ; Viruses - genetics
É parte de: Molecular ecology resources, 2024-02, Vol.24 (2), p.e13904-n/a
Notas: Ulisses Rocha and Jonas Coelho Kasmanas should be considered joint first author.
Acknowledgements
CLUE‐TERRA Consortium group members are included in
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Descrição: 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.
Editor: England: Wiley Subscription Services, Inc
Idioma: Inglês

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MuDoGeR: Multi‐Domain Genome recovery from metagenomes made easy

England: Wiley Subscription Services, Inc

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