Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

The Critical Assessment of Metagenome Interpretation (CAMI) community initiative presents results from its first challenge, a rigorous benchmarking of software for metagenome assembly, binning and taxonomic profiling. Methods for assembly, taxonomic profiling and binning are key to interpreting meta...

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Published inNature methods Vol. 14; no. 11; pp. 1063 - 1071
Main Authors 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
Format Journal Article
LanguageEnglish
Published New York Nature Publishing Group US 01.11.2017
Nature Publishing Group
Subjects
49/23
631/114
631/114/1386
631/326/2565/2142
Algorithms
analysis
Assembly
BASIC BIOLOGICAL SCIENCES
Benchmarking
Benchmarks
Biochemistry & Molecular Biology
Biodiversity
Bioinformatics
Biological Microscopy
Biological Techniques
Biomedical and Life Sciences
Biomedical Engineering/Biotechnology
Computer programs
Critical care medicine
Genomes
Life Sciences
MATHEMATICS AND COMPUTING
Metagenomics
Microorganisms
Performance assessment
Plasmids
Proteomics
Reproducibility
Sequence Analysis, DNA
Software
Taxonomy
Online AccessGet full text

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Abstract The Critical Assessment of Metagenome Interpretation (CAMI) community initiative presents results from its first challenge, a rigorous benchmarking of software for metagenome assembly, binning and taxonomic profiling. 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.
AbstractList 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.
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.
The Critical Assessment of Metagenome Interpretation (CAMI) community initiative presents results from its first challenge, a rigorous benchmarking of software for metagenome assembly, binning and taxonomic profiling. 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.
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 [similar]700 newly sequenced microorganisms and [similar]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.
Audience Academic
Author Quince, Christopher
Klenk, Hans-Peter
Wu, Yu-Wei
Sczyrba, Alexander
Balvočiūtė, Monika
Lingner, Thomas
Jørgensen, Tue Sparholt
Jain, Chirag
Nagarajan, Niranjan
Darling, Aaron E
Rattei, Thomas
Strous, Marc
Chia, Burton K H
Schulze-Lefert, Paul
Woyke, Tanja
Fritz, Adrian
Dröge, Johannes
Blood, Philip D
Dahms, Eik
Renard, Bernhard Y
Barton, Michael D
Edwards, Robert A
Göker, Markus
McHardy, Alice C
Pop, Mihai
Fiedler, Jessika
Lin, Hsin-Hung
Majda, Stephan
Vorholt, Julia A
Rubin, Edward M
Hofmann, Peter
Wang, Zhong
Rizk, Guillaume
Meyer, Fernando
Cuevas, Daniel A
Denis, Bertrand
Turaev, Dmitrij
Deltel, Charles
Egan, Robert
Bai, Yang
Garrido-Oter, Ruben
Don Kang, Dongwan
Bremges, Andreas
Janssen, Stefan
Lavenier, Dominique
DeMaere, Matthew Z
Shapiro, Nicole
Gurevich, Alexey
Chikhi, Rayan
Singer, Steven W
Koslicki, David
Belmann, Peter
Kyrpides, Nikos C
Silva, Genivaldo Gueiros Z
Klingenberg, Heiner
Saha, Surya
Sørensen, Søren J
Froula, Jeff L
Lemaitre, Claire
Hansen, Lars Hestbjerg
Cook, Jeffrey J
Gregor, Ivan
Meinicke, Peter
Peterlongo, Pierre
Liao, Yu
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/28967888$$D View this record in MEDLINE/PubMed
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10.1126/scitranslmed.aad0917
10.1093/nar/gkm864
10.1038/nmeth.3837
10.1073/pnas.0409727102
10.1093/bioinformatics/btv697
10.1093/bioinformatics/btv033
10.1093/bioinformatics/btu320
10.1038/nmeth1043
10.7717/peerj.1603
10.1186/gb-2014-15-3-r46
10.1186/s12864-017-3501-4
10.1038/nature11234
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COPYRIGHT 2017 Nature Publishing Group
Copyright Nature Publishing Group Nov 2017
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CorporateAuthor Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Univ. of California, Oakland, CA (United States)
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Snippet The Critical Assessment of Metagenome Interpretation (CAMI) community initiative presents results from its first challenge, a rigorous benchmarking of software...
Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmarking complicates...
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SubjectTerms 49/23
631/114
631/114/1386
631/326/2565/2142
Algorithms
analysis
Assembly
BASIC BIOLOGICAL SCIENCES
Benchmarking
Benchmarks
Biochemistry & Molecular Biology
Biodiversity
Bioinformatics
Biological Microscopy
Biological Techniques
Biomedical and Life Sciences
Biomedical Engineering/Biotechnology
Computer programs
Critical care medicine
Genomes
Life Sciences
MATHEMATICS AND COMPUTING
Metagenomics
Microorganisms
Performance assessment
Plasmids
Proteomics
Reproducibility
Sequence Analysis, DNA
Software
Taxonomy
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Title Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software
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