MuDoGeR: Multi-Domain Genome Recovery from metagenomes made easy

Nunes da Rocha, U.; Kasmanas, J.; Kallies, R.; Saraiva, J. P.; Brizola Toscan, R.; Stefanic, P.; Bicalho, M. F.; Correa, F. B.; Basturk, M. N.; Fousekis, E.; Barbosa, L. M. V.; Plewka, J.; Probst, A. J.; Baldrian, P.; Stadler, P. F.; CoLlaborative mUlti-domain Exploration of TERRestriAl metagenomes (CLUE-TERRA),

doi:10.1101/2022.06.21.496983

bioRxiv · 10.1101/2022.06.21.496983

MuDoGeR: Multi-Domain Genome Recovery from metagenomes made easy

Nunes da Rocha, U.·Kasmanas, J.·Kallies, R.·Saraiva, J. P.·Brizola Toscan, R.·Stefanic, P.·Bicalho, M. F.·Correa, F. B.·Basturk, M. N.·Fousekis, E.·Barbosa, L. M. V.·Plewka, J.·Probst, A. J.·Baldrian, P.·Stadler, P. F.·CoLlaborative mUlti-domain Exploration of TERRestriAl metagenomes (CLUE-TERRA),

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Abstract

Several computational frameworks and workflows that recover genomes from prokaryotes, eukaryotes, and viruses from metagenomes exist. However, 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 accessible for non-bioinformaticians that make 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. MuDoGeR is open-source software available at https://github.com/mdsufz/MuDoGeR.

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Nunes da Rocha, U., Kasmanas, J., Kallies, R., Saraiva, J. P., Brizola Toscan, R., Stefanic, P., Bicalho, M. F., Correa, F. B., Basturk, M. N., Fousekis, E., Barbosa, L. M. V., Plewka, J., Probst, A. J., Baldrian, P., Stadler, P. F., CoLlaborative mUlti-domain Exploration of TERRestriAl metagenomes (CLUE-TERRA),. 2022-06-21. MuDoGeR: Multi-Domain Genome Recovery from metagenomes made easy. https://doi.org/10.1101/2022.06.21.496983

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