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Critical assessment of metagenome interpretation - a benchmark of metagenomics software

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Sczyrba, Alexander, Hofmann, Peter, Belmann, Peter, Koslicki, David, Janssen, Stefan, Dröge, Johannes, Gregor, Ivan, Majda, Stephan, Fiedler, Jessika, Dahms, Eik et al.
(2017) Critical assessment of metagenome interpretation - a benchmark of metagenomics software. Nature Methods, 14 (11). pp. 1063-1071. doi:10.1038/nmeth.4458

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Official URL: http://dx.doi.org/10.1038/nmeth.4458

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Abstract

Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmarking complicates performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups. Assembly and genome binning programs performed well for species represented by individual genomes but were substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below family level. Parameter settings markedly affected performance, underscoring their importance for program reproducibility. The CAMI results highlight current challenges but also provide a roadmap for software selection to answer specific research questions.

Item Type: Journal Article
Divisions: Faculty of Medicine > Warwick Medical School > Biomedical Sciences
Faculty of Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection
Faculty of Medicine > Warwick Medical School
Journal or Publication Title: Nature Methods
Publisher: Nature Publishing Group
ISSN: 1548-7091
Official Date: 2 October 2017
Dates:
DateEvent
2 October 2017Published
25 August 2017Accepted
Date of first compliant deposit: 18 October 2018
Volume: 14
Number: 11
Page Range: pp. 1063-1071
DOI: 10.1038/nmeth.4458
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access

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