A probabilistic model to recover individual genomes from metagenomes

Dröge J, Schönhuth A, McHardy AC (2017)
PeerJ Computer Science 3: e117.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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DOI
Autor*in
Dröge, Johannes; Schönhuth, AlexanderUniBi ; McHardy, Alice C.
Einrichtung
Technische Fakultät > AG Genome Data Science
Abstract / Bemerkung
Shotgun metagenomics of microbial communities reveal information about strains of relevance for applications in medicine, biotechnology and ecology. Recovering their genomes is a crucial but very challenging step due to the complexity of the underlying biological system and technical factors. Microbial communities are heterogeneous, with oftentimes hundreds of present genomes deriving from different species or strains, all at varying abundances and with different degrees of similarity to each other and reference data. We present a versatile probabilistic model for genome recovery and analysis, which aggregates three types of information that are commonly used for genome recovery from metagenomes. As potential applications we showcase metagenome contig classification, genome sample enrichment and genome bin comparisons. The open source implementation MGLEX is available via the Python Package Index and on GitHub and can be embedded into metagenome analysis workflows and programs.
Erscheinungsjahr
2017
Zeitschriftentitel
PeerJ Computer Science
Band
3
Art.-Nr.
e117
eISSN
2376-5992
Page URI
https://pub.uni-bielefeld.de/record/2941785

Zitieren

Dröge J, Schönhuth A, McHardy AC. A probabilistic model to recover individual genomes from metagenomes. PeerJ Computer Science. 2017;3: e117.
Dröge, J., Schönhuth, A., & McHardy, A. C. (2017). A probabilistic model to recover individual genomes from metagenomes. PeerJ Computer Science, 3, e117. doi:10.7717/peerj-cs.117
Dröge, Johannes, Schönhuth, Alexander, and McHardy, Alice C. 2017. “A probabilistic model to recover individual genomes from metagenomes”. PeerJ Computer Science 3: e117.
Dröge, J., Schönhuth, A., and McHardy, A. C. (2017). A probabilistic model to recover individual genomes from metagenomes. PeerJ Computer Science 3:e117.
Dröge, J., Schönhuth, A., & McHardy, A.C., 2017. A probabilistic model to recover individual genomes from metagenomes. PeerJ Computer Science, 3: e117.
J. Dröge, A. Schönhuth, and A.C. McHardy, “A probabilistic model to recover individual genomes from metagenomes”, PeerJ Computer Science, vol. 3, 2017, : e117.
Dröge, J., Schönhuth, A., McHardy, A.C.: A probabilistic model to recover individual genomes from metagenomes. PeerJ Computer Science. 3, : e117 (2017).
Dröge, Johannes, Schönhuth, Alexander, and McHardy, Alice C. “A probabilistic model to recover individual genomes from metagenomes”. PeerJ Computer Science 3 (2017): e117.
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