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Title: Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

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.

Authors:
 [1];  [2];  [3];  [4];  [5];  [2];  [2];  [6];  [7];  [8];  [9];  [10];  [11];  [12];  [13];  [14];  [15];  [16];  [17];  [18] more »;  [19];  [20];  [21];  [10];  [22];  [23];  [24];  [20];  [20];  [13];  [13];  [13];  [13];  [25];  [26];  [27];  [26];  [26];  [28];  [29];  [30];  [31];  [32];  [33];  [34];  [34];  [13];  [35];  [36];  [36];  [37];  [37];  [37];  [38];  [39];  [40];  [41];  [42];  [43];  [13];  [13];  [44];  [45];  [13]; ORCiD logo [18]; ORCiD logo [17]; ORCiD logo [46] « less
  1. Bielefeld Univ., Bielefeld (Germany)
  2. Heinrich Heine Univ. (HHU), Duesseldorf (Germany); Helmholtz Centre for Infection Research (HZI), Braunschweig (Germany); Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, (Germany)
  3. Bielefeld Univ., Bielefeld (Germany); Helmholtz Centre for Infection Research (HZI), Braunschweig (Germany); Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, (Germany)
  4. Oregon State Univ., Corvallis, OR (United States)
  5. Helmholtz Centre for Infection Research (HZI), Braunschweig (Germany); Univ. of California, San Diego, CA (United States)
  6. Heinrich Heine Univ. (HHU), Duesseldorf (Germany)
  7. Heinrich Heine Univ. (HHU), Duesseldorf (Germany); Helmholtz Centre for Infection Research (HZI), Braunschweig (Germany)
  8. Heinrich Heine Univ. (HHU), Duesseldorf (Germany); Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, (Germany)
  9. Bielefeld Univ., Bielefeld (Germany); Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, (Germany); German Center for Infection Research (DZIF), Braunschweig (Germany)
  10. Helmholtz Centre for Infection Research (HZI), Braunschweig (Germany); Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, (Germany)
  11. Heinrich Heine Univ. (HHU), Duesseldorf (Germany); Helmholtz Centre for Infection Research (HZI), Braunschweig (Germany); Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, (Germany); Max Planck Inst. for Plant Breeding Research, Cologne (Germany). Cluster of Excellence on Plant Sciences (CEPLAS)
  12. Aarhus Univ., Roskilde (Denmark); Univ. of Copenhagen (Denmark); Roskilde Univ., Roskilde (Denmark)
  13. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  14. Carnegie Mellon Univ., Pittsburgh, PA (United States)
  15. Saint Petersburg State Univ., Saint Petersburg (Russia)
  16. Max Planck Inst. for Plant Breeding Research, Cologne (Germany)
  17. Univ. of Vienna (Austria)
  18. Univ. of Technology Sydney, Sydney, NSW (Australia)
  19. Research Center in Computer Science (CRIStAL), Lille (France); National Centre of the Scientific Research (CNRS), Rennes (France)
  20. Genome Inst. of Singapore (Singapore)
  21. Univ. of Warwick, Coventry (United Kingdom)
  22. Univ. of Tuebingen, Tuebingen (Germany)
  23. Aarhus Univ., Roskilde (Denmark)
  24. Univ. of Copenhagen (Denmark)
  25. Intel Corporation, Hillsboro, OR (United States)
  26. Inria Rennes—Bretagne Atlantique Research Centre, Rennes (France); Inst. of Research in Informatics and Random Systems (IRISA), Rennes (France)
  27. Helmholtz Centre for Infection Research, Braunschweig (Germany)
  28. Inst. of Research in Informatics and Random Systems (IRISA), Rennes (France); Algorizk–IT consulting and software systems, Paris (France)
  29. National Centre of the Scientific Research (CNRS), Rennes (France); Inst. of Research in Informatics and Random Systems (IRISA), Rennes (France)
  30. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Taipei Medical Univ., Taipei (Taiwan)
  31. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  32. Georgia Inst. of Technology, Atlanta, GA (United States)
  33. Univ. of Calgary, AB (Canada)
  34. Univ. of Goettingen (Germany). Inst. for Microbiology and Genetics
  35. Genevention GmbH, Goettingen (Germany)
  36. National Health Research Inst., Zhunan Town (Taiwan)
  37. San Diego State Univ., San Diego, CA (United States)
  38. Boyce Thompson Inst. for Plant Research, New York, NY (United States)
  39. Robert Koch Inst., Berlin (Germany); Coordination for the Improvement of Higher Education Personnel (CAPES) Foundation, Ministry of Education of Brazil, Brasília (Brazil)
  40. Robert Koch Inst., Berlin (Germany)
  41. Univ. of Maryland, College Park, MD (United States)
  42. Newcastle Univ., Newcastle upon Tyne (United Kingdom)
  43. Leibniz Inst. DSMZ, Braunschweig (Germany). German Collection of Microorganisms and Cell Cultures
  44. Federal Inst. of Technology, Zurich (Switzerland)
  45. Max Planck Inst. for Plant Breeding Research, Cologne (Germany). Cluster of Excellence on Plant Sciences (CEPLAS)
  46. Heinrich Heine Univ. (HHU), Duesseldorf (Germany). Cluster of Excellence on Plant Sciences (CEPLAS); Helmholtz Centre for Infection Research (HZI), Braunschweig (Germany); Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, (Germany)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1543734
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Nature Methods
Additional Journal Information:
Journal Volume: 14; Journal Issue: 11; Journal ID: ISSN 1548-7091
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING; Biochemistry & Molecular Biology

Citation Formats

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, Balvočiūtė, 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. Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software. United States: N. p., 2017. Web. doi:10.1038/nmeth.4458.
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, Balvočiūtė, 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, & McHardy, Alice C. Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software. United States. doi:10.1038/nmeth.4458.
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, Balvočiūtė, 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. Mon . "Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software". United States. doi:10.1038/nmeth.4458. https://www.osti.gov/servlets/purl/1543734.
@article{osti_1543734,
title = {Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software},
author = {Sczyrba, Alexander and Hofmann, Peter and Belmann, Peter and Koslicki, David and Janssen, Stefan and Dröge, Johannes and Gregor, Ivan and Majda, Stephan and Fiedler, Jessika and Dahms, Eik and Bremges, Andreas and Fritz, Adrian and Garrido-Oter, Ruben and Jørgensen, Tue Sparholt and Shapiro, Nicole and Blood, Philip D. and Gurevich, Alexey and Bai, Yang and Turaev, Dmitrij and DeMaere, Matthew Z. and Chikhi, Rayan and Nagarajan, Niranjan and Quince, Christopher and Meyer, Fernando and Balvočiūtė, Monika and Hansen, Lars Hestbjerg and Sørensen, Søren J. and Chia, Burton K. H. and Denis, Bertrand and Froula, Jeff L. and Wang, Zhong and Egan, Robert and Don Kang, Dongwan and Cook, Jeffrey J. and Deltel, Charles and Beckstette, Michael and Lemaitre, Claire and Peterlongo, Pierre and Rizk, Guillaume and Lavenier, Dominique and Wu, Yu-Wei and Singer, Steven W. and Jain, Chirag and Strous, Marc and Klingenberg, Heiner and Meinicke, Peter and Barton, Michael D. and Lingner, Thomas and Lin, Hsin-Hung and Liao, Yu-Chieh and Silva, Genivaldo Gueiros Z. and Cuevas, Daniel A. and Edwards, Robert A. and Saha, Surya and Piro, Vitor C. and Renard, Bernhard Y. and Pop, Mihai and Klenk, Hans-Peter and Göker, Markus and Kyrpides, Nikos C. and Woyke, Tanja and Vorholt, Julia A. and Schulze-Lefert, Paul and Rubin, Edward M. and Darling, Aaron E. and Rattei, Thomas and McHardy, Alice C.},
abstractNote = {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.},
doi = {10.1038/nmeth.4458},
journal = {Nature Methods},
number = 11,
volume = 14,
place = {United States},
year = {2017},
month = {10}
}

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