Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software

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

doi:10.1038/nmeth.4458

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software

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

研究成果: 雜誌貢獻 › 文章 › 同行評審

474 引文斯高帕斯（Scopus）

摘要

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.

原文	英語
頁（從 - 到）	1063-1071
頁數	9
期刊	Nature Methods
卷	14
發行號	11
DOIs	https://doi.org/10.1038/nmeth.4458
出版狀態	已發佈 - 11月 2017

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10.1038/nmeth.4458

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Sczyrba, A., Hofmann, P., Belmann, P., Koslicki, D., Janssen, S., Dröge, J., Gregor, I., Majda, S., Fiedler, J., Dahms, E., Bremges, A., Fritz, A., Garrido-Oter, R., Jørgensen, T. S., Shapiro, N., Blood, P. D., Gurevich, A., Bai, Y., Turaev, D., ... McHardy, A. C. (2017). Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software. Nature Methods, 14(11), 1063-1071. https://doi.org/10.1038/nmeth.4458

Sczyrba, A, Hofmann, P, Belmann, P, Koslicki, D, Janssen, S, Dröge, J, Gregor, I, Majda, S, Fiedler, J, Dahms, E, Bremges, A, Fritz, A, Garrido-Oter, R, Jørgensen, TS, Shapiro, N, Blood, PD, Gurevich, A, Bai, Y, Turaev, D, DeMaere, MZ, Chikhi, R, Nagarajan, N, Quince, C, Meyer, F, Balvočiūtė, M, Hansen, LH, Sørensen, SJ, Chia, BKH, Denis, B, Froula, JL, Wang, Z, Egan, R, Don Kang, D, Cook, JJ, Deltel, C, Beckstette, M, Lemaitre, C, Peterlongo, P, Rizk, G, Lavenier, D, Wu, Y-W, Singer, SW, Jain, C, Strous, M, Klingenberg, H, Meinicke, P, Barton, MD, Lingner, T, Lin, H-H, Liao, Y-C, Silva, GGZ, Cuevas, DA, Edwards, RA, Saha, S, Piro, VC, Renard, BY, Pop, M, Klenk, H-P, Göker, M, Kyrpides, NC, Woyke, T, Vorholt, JA, Schulze-Lefert, P, Rubin, EM, Darling, AE, Rattei, T & McHardy, AC 2017, 'Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software', Nature Methods, 卷 14, 編號 11, 頁 1063-1071. https://doi.org/10.1038/nmeth.4458

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AU - Don Kang, Dongwan

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Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software

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