ArticleNature methods2017
Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.
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Article in Nature methods, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 458 papers.
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458citing papers in PubMed
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Who cites it
458 citing papers in PubMed.
- Integrating multi-omics technologies to decipher microbiome functions.Nature communications · 2026Review
- The Biotechnological Applications of Marine Bacteria.Biology · 2026Review
- metaWEPP: leveraging biobank-scale intra-species phylogenies for near-haplotype resolution in metagenomic analysis.NAR genomics and bioinformatics · 2026Article
- Hunting for Helminths: short- and long-read shotgun metagenomics for helminth detection in faecal samples.PLoS neglected tropical diseases · 2026Article
- Comparative metagenomic assessment of Illumina-compatible library preparation methods, short-read lengths, and PacBio HiFi sequencing reveals differences in microbial and functional diversity recovery from a complex environmental sample.Microbiology spectrum · 2026Article
- Benchmarking methods for extracting microbial signal from host-dominated metatranscriptomes.Briefings in bioinformatics · 2026Article
- Sarand: exploring antimicrobial resistance gene neighbourhoods in complex metagenomic assembly graphs.NAR genomics and bioinformatics · 2026Article
- A damage-aware NGS workflow for conservative species identification from ultra-degraded DNA.Analytical and bioanalytical chemistry · 2026Article
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- Behavioral and Functional Profiling ofbioRxiv : the preprint server for biology · 2026Article
- Reliable evaluation and learning in multi-input biological association prediction.Briefings in bioinformatics · 2026Article
- Predicting functions of uncharacterized gene products from microbial communities.Nature biotechnology · 2026Article
- Responsible Use of Large Language Models in Microbial Genomics and Bioinformatics: A Life-Science Framework for Reliability, Reproducibility, and Risk-Aware Interpretation.Life (Basel, Switzerland) · 2026Review
- Quantitative evaluation of microbiome sequencing resolution under varying experimental conditions using defined mock communities.Scientific reports · 2026Article
- Dual-platform metagenomic surveillance distinguishes pathogen and resistome hotspots across agricultural and mixed-use watersheds.One health (Amsterdam, Netherlands) · 2026Article
- Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper.Nature biotechnology · 2026Article
- Benchmarking the impact of reference genome selection on taxonomic profiling accuracy.BMC genomics · 2026Article
- Metagenomics provides broad detection of pathogens, antimicrobial resistance, and virulence genes in pig diarrhoea and complement conventional methods.Animal microbiome · 2026Article
- Enhancing inference of differential gene expression in metatranscriptomes from human microbial communities.Nature communications · 2026Article
398 more citing papers are in PubMed but not listed here.
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Authors and funding
67 authors.
Alexander SczyrbaFaculty of Technology, Bielefeld University, Bielefeld, Germany.
Peter HofmannFormerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany.
Peter BelmannFaculty of Technology, Bielefeld University, Bielefeld, Germany.
David KoslickiMathematics Department, Oregon State University, Corvallis, Oregon, USA.
Stefan JanssenDepartment of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.
Johannes DrögeFormerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany.
Ivan GregorFormerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany.
Stephan MajdaFormerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany.
Jessika FiedlerFormerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany.
Eik DahmsFormerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany.
Andreas BremgesFaculty of Technology, Bielefeld University, Bielefeld, Germany.
Adrian FritzDepartment of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.
Ruben Garrido-OterFormerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany.
Tue Sparholt JørgensenDepartment of Environmental Science, Section of Environmental microbiology and Biotechnology, Aarhus University, Roskilde, Denmark.
Nicole ShapiroDepartment of Energy, Joint Genome Institute, Walnut Creek, California, USA.
Philip D BloodPittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
Alexey GurevichCenter for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia.
Yang BaiDepartment of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
Dmitrij TuraevDepartment of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
Matthew Z DeMaereThe ithree institute, University of Technology Sydney, Sydney, New South Wales, Australia.
Rayan ChikhiDepartment of Computer Science, Research Center in Computer Science (CRIStAL), Signal and Automatic Control of Lille, Lille, France.
Niranjan NagarajanDepartment of Computational and Systems Biology, Genome Institute of Singapore, Singapore.
Christopher QuinceDepartment of Microbiology and Infection, Warwick Medical School, University of Warwick, Coventry, UK.
Fernando MeyerDepartment of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.
Monika BalvočiūtėDepartment of Computer Science, University of Tuebingen, Tuebingen, Germany.
Lars Hestbjerg HansenDepartment of Environmental Science, Section of Environmental microbiology and Biotechnology, Aarhus University, Roskilde, Denmark.
Søren J SørensenDepartment of Microbiology, University of Copenhagen, Copenhagen, Denmark.
Burton K H ChiaDepartment of Computational and Systems Biology, Genome Institute of Singapore, Singapore.
Bertrand DenisDepartment of Computational and Systems Biology, Genome Institute of Singapore, Singapore.
Jeff L FroulaDepartment of Energy, Joint Genome Institute, Walnut Creek, California, USA.
Zhong WangDepartment of Energy, Joint Genome Institute, Walnut Creek, California, USA.
Robert EganDepartment of Energy, Joint Genome Institute, Walnut Creek, California, USA.
Dongwan Don KangDepartment of Energy, Joint Genome Institute, Walnut Creek, California, USA.
Jeffrey J CookIntel Corporation, Hillsboro, Oregon, USA.
Charles DeltelGenScale-Bioinformatics Research Team, Inria Rennes-Bretagne Atlantique Research Centre, Rennes, France.
Michael BeckstetteDepartment of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany.
Claire LemaitreGenScale-Bioinformatics Research Team, Inria Rennes-Bretagne Atlantique Research Centre, Rennes, France.
Pierre PeterlongoGenScale-Bioinformatics Research Team, Inria Rennes-Bretagne Atlantique Research Centre, Rennes, France.
Guillaume RizkInstitute of Research in Informatics and Random Systems (IRISA), Rennes, France.
Dominique LavenierNational Centre of the Scientific Research (CNRS), Rennes, France.
Yu-Wei WuJoint BioEnergy Institute, Emeryville, California, USA.
Steven W SingerJoint BioEnergy Institute, Emeryville, California, USA.
Chirag JainSchool of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA.
Marc StrousEnergy Engineering and Geomicrobiology, University of Calgary, Calgary, Alberta, Canada.
Heiner KlingenbergDepartment of Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany.
Peter MeinickeDepartment of Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany.
Michael D BartonDepartment of Energy, Joint Genome Institute, Walnut Creek, California, USA.
Thomas LingnerGenevention GmbH, Goettingen, Germany.
Hsin-Hung LinInstitute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Taiwan.
Yu-Chieh LiaoInstitute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Taiwan.
Genivaldo Gueiros Z SilvaComputational Science Research Center, San Diego State University, San Diego, California, USA.
Daniel A CuevasComputational Science Research Center, San Diego State University, San Diego, California, USA.
Robert A EdwardsComputational Science Research Center, San Diego State University, San Diego, California, USA.
Surya SahaBoyce Thompson Institute for Plant Research, New York, New York, USA.
Vitor C PiroResearch Group Bioinformatics (NG4), Robert Koch Institute, Berlin, Germany.
Bernhard Y RenardResearch Group Bioinformatics (NG4), Robert Koch Institute, Berlin, Germany.
Mihai PopCenter for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA.
Hans-Peter KlenkSchool of Biology, Newcastle University, Newcastle upon Tyne, UK.
Markus GökerLeibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Nikos C KyrpidesDepartment of Energy, Joint Genome Institute, Walnut Creek, California, USA.
Tanja WoykeDepartment of Energy, Joint Genome Institute, Walnut Creek, California, USA.
Julia A VorholtInstitute of Microbiology, ETH Zurich, Zurich, Switzerland.
Paul Schulze-LefertDepartment of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
Edward M RubinDepartment of Energy, Joint Genome Institute, Walnut Creek, California, USA.
Aaron E DarlingThe ithree institute, University of Technology Sydney, Sydney, New South Wales, Australia.ORCID http://orcid.org/0000-0003-2397-7925
Thomas RatteiDepartment of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.ORCID http://orcid.org/0000-0002-0592-7791
Alice C McHardyFormerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany.ORCID http://orcid.org/0000-0003-2370-3430
Funding
Algorithms and Software for the Assembly of Metagenomic DataR01AI100947 · NIAID · UNIV OF MARYLAND, COLLEGE PARK · PI POP, MIHAI · 2013 to 2025
$7.4MBiotechnology and Biological Sciences Research Council BB/L027801/1Medical Research Council MR/L015080/1Medical Research Council MR/M50161X/1NIAID NIH HHS R01 AI100947
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.
Indexed as
MetagenomicsSoftwareAlgorithmsBenchmarkingSequence Analysis, DNA
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