Critical assessment of metagenome interpretation - A benchmark of metagenomics software

Sczyrba, Alexander, Hofmann, Peter, Belmann, Peter, Koslicki, David, Janssen, Stefan, Dröge, Johannes, Gregor, Ivan, Majda, Stephan, Fiedler, Jessika, Dahms, Eik, Bremges, Andreas, Fritz, Adrian, Garrido-Oter, Ruben, Jørgensen, Tue Sparholt, Shapiro, Nicole, Blood, Philip D., Gurevich, Alexey, Bai, Yang, Turaev, Dmitrij, Demaere, Matthew Z., Chikhi, Rayan, Nagarajan, Niranjan, Quince, Christopher, Meyer, Fernando, Balvočiutė, Monika, Hansen, Lars Hestbjerg, Sørensen, Søren J., Chia, Burton K. H., Denis, Bertrand, Froula, Jeff L., Wang, Zhong, Egan, Robert, Don Kang, Dongwan, Cook, Jeffrey J., Deltel, Charles, Beckstette, Michael, Lemaitre, Claire, Peterlongo, Pierre, Rizk, Guillaume, Lavenier, Dominique, Wu, Yu Wei, Singer, Steven W., Jain, Chirag, Strous, Marc, Klingenberg, Heiner, Meinicke, Peter, Barton, Michael D., Lingner, Thomas, Lin, Hsin Hung, Liao, Yu Chieh, Silva, Genivaldo Gueiros Z., Cuevas, Daniel A., Edwards, Robert A., Saha, Surya, Piro, Vitor C., Renard, Bernhard Y., Pop, Mihai, Klenk, Hans Peter, Göker, Markus, Kyrpides, Nikos C., Woyke, Tanja, Vorholt, Julia A., Schulze-Lefert, Paul, Rubin, Edward M., Darling, Aaron E., Rattei, Thomas and McHardy, Alice C. (2017) Critical assessment of metagenome interpretation - A benchmark of metagenomics software. Nature Methods, 14 (11). pp. 1063-1071. ISSN 1548-7091

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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: Article
Additional Information: Funding Information: We thank C. Della Beffa, J. Alneberg, D. Huson and P. Grupp for their input, and the Isaac Newton Institute for Mathematical Sciences for its hospitality during the MTG program (supported by UK Engineering and Physical Sciences Research Council (EPSRC) grant EP/K032208/1). Sequencing at the US Department of Energy Joint Genome Institute was supported under contract DE-AC02-05CH11231. R.G.O. was supported by the Cluster of Excellence on Plant Sciences program of the Deutsche Forschungsgemeinschaft; A.E.D. and M.Z.D., through the Australian Research Council’s Linkage Projects (LP150100912); J.A.V., by the European Research Council advanced grant (PhyMo); D.B., B.K.H.C. and N.N., by the Agency for Science, Technology and Research (A*STAR), Singapore; T.S.J., by the Lundbeck Foundation (project DK nr R44-A4384); L.H.H. by a VILLUM FONDEN Block Stipend on Mobilomics; and P.D.B. by the National Science Foundation (NSF, grant DBI-1458689). This work used the Bridges and Blacklight systems, supported by NSF awards ACI-1445606 and Funding Information: ACI-1041726, respectively, at the Pittsburgh Supercomputing Center (PSC), under the Extreme Science and Engineering Discovery Environment (XSEDE), supported by NSF grant OCI-1053575.
Uncontrolled Keywords: biotechnology,biochemistry,molecular biology,cell biology ,/dk/atira/pure/subjectarea/asjc/1300/1305
Faculty \ School: Faculty of Science > School of Biological Sciences
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Depositing User: LivePure Connector
Date Deposited: 08 Sep 2022 15:30
Last Modified: 29 Sep 2022 18:31
URI: https://ueaeprints.uea.ac.uk/id/eprint/87984
DOI: 10.1038/nmeth.4458

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