ArticleNature methods2022
Critical Assessment of Metagenome Interpretation: the second round of challenges.
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Article in Nature methods, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 219 papers, 1 of them a synthesis that pooled it.
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219citing papers in PubMed, 1 pooled it
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Who cites it
219 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Packaging and containerization of computational methods.Nature protocols · 2024Pooled it
- metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.Gut microbes · 2026Article
- Perseus: lineage-aware refinement of Kraken2 taxonomic classification for long read metagenomes.Bioinformatics (Oxford, England) · 2026Article
- Problems With GO Enrichment as an Endpoint for Ecological Omics Interpretation.Molecular ecology · 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
- 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
- Phage bioinformatics tools: a review of computational approaches for bacteriophage research.Briefings in bioinformatics · 2026Review
- Benchmarking methods for extracting microbial signal from host-dominated metatranscriptomes.Briefings in bioinformatics · 2026Article
- Deployable high-fidelity metagenome binning at scale with QuickBin.Communications biology · 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
- Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper.Nature biotechnology · 2026Article
- Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities.Science advances · 2026Article
- Benchmarking the impact of reference genome selection on taxonomic profiling accuracy.BMC genomics · 2026Article
- Metabolic reprogramming of the infant gut by bifidobacteria-based probiotics drives exclusion of antibiotic-resistant pathobionts.Cell reports. Medicine · 2026Article
- Plant-associated fungi co-opt ancient antimicrobials for host manipulation.Science advances · 2026Article
- Benchmarking shotgun metagenomics.Nature microbiology · 2026Article
- Rapid phylogenomic analysis for viral surveillance and metagenomic profiling with Omni2Tree.bioRxiv : the preprint server for biology · 2026Article
- TIPP-SD: A new method for species detection in microbiomes.PLoS computational biology · 2026Article
- Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis.Nature microbiology · 2026Article
159 more citing papers are in PubMed but not listed here.
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Authors and funding
103 authors.
Fernando Meyer *Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.ORCID http://orcid.org/0000-0002-0901-3815
Adrian Fritz *Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.ORCID http://orcid.org/0000-0002-9853-5577
Zhi-Luo DengComputational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.
David KoslickiPennsylvania State University, State College, PA, USA.ORCID http://orcid.org/0000-0002-0640-954X
Till Robin LeskerGerman Center for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany.
Alexey GurevichSaint Petersburg State University, Saint Petersburg, Russia.ORCID http://orcid.org/0000-0002-5855-3519
Gary RobertsonComputational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.
Mohammed AlserDepartment of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland.
Dmitry AntipovCenter for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia.
Francesco BeghiniDepartment CIBIO, University of Trento, Trento, Italy.ORCID http://orcid.org/0000-0002-8105-9607
Denis BertrandGenome Institute of Singapore, Singapore, Singapore.
Jaqueline J BritoUniversity of Southern California, Los Angeles, CA, USA.
C Titus BrownUniversity of California, Davis, Davis, CA, USA.ORCID http://orcid.org/0000-0001-6001-2677
Jan BuchmannInstitute for Biological Data Science, Heinrich-Heine-University, Düsseldorf, Germany.ORCID http://orcid.org/0000-0002-6842-1229
Aydin BuluçLawrence Berkeley National Laboratory, Berkeley, CA, USA.
Bo ChenLawrence Berkeley National Laboratory, Berkeley, CA, USA.
Rayan ChikhiInstitut Pasteur, Paris, France.ORCID http://orcid.org/0000-0003-1099-8735
Philip T L C ClausenNational Food Institute, Division of Global Surveillance, Technical University of Denmark, Lyngby, Denmark.ORCID http://orcid.org/0000-0002-8197-7520
Alexandru CristianDrexel University, Philadelphia, PA, USA.
Piotr Wojciech DabrowskiRobert Koch-Institut, Berlin, Germany.ORCID http://orcid.org/0000-0003-4893-805X
Aaron E DarlingUniversity of Technology Sydney, Sydney, Australia.ORCID http://orcid.org/0000-0003-2397-7925
Rob EganDOE Joint Genome Institute, Berkeley, CA, USA.
Eleazar EskinUniversity of California, Los Angeles, Los Angeles, CA, USA.
Evangelos GeorganasIntel Corporation, Santa Clara, CA, USA.
Eugene GoltsmanDOE Joint Genome Institute, Berkeley, CA, USA.
Melissa A GrayDrexel University, Philadelphia, PA, USA.
Lars Hestbjerg HansenUniversity of Copenhagen, Department of Plant and Environmental Science, Frederiksberg, Denmark.
Steven HofmeyrLawrence Berkeley National Laboratory, Berkeley, CA, USA.
Pingqin HuangSchool of Computer Science, Fudan University, Shanghai, China.
Luiz IrberUniversity of California, Davis, Davis, CA, USA.
Huijue JiaBGI-Shenzhen, Shenzhen, China.
Tue Sparholt JørgensenTechnical University of Denmark, Novo Nordisk Foundation Center for Biosustainability, Lyngby, Denmark.ORCID http://orcid.org/0000-0002-2437-7086
Silas D KieserDepartment of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland.ORCID http://orcid.org/0000-0002-5935-9734
Terje KlemetsenThe Arctic University of Norway, Tromsø, Norway.
Axel KolaCharité-Universitätsmedizin Berlin, Berlin, Germany.
Mikhail KolmogorovDepartment of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA.
Anton KorobeynikovCenter for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia.ORCID http://orcid.org/0000-0002-2937-9259
Jason KwanUniversity of Wisconsin-Madison, Madison, WI, USA.
Nathan LaPierreUniversity of California, Los Angeles, Los Angeles, CA, USA.
Claire LemaitreUniv. Rennes, Inria, CNRS, IRISA, Rennes, France.ORCID http://orcid.org/0000-0001-8675-170X
Chenhao LiGenome Institute of Singapore, Singapore, Singapore.
Antoine LimassetUniversité Lille, CNRS, CRIStAL, Lille, France.ORCID http://orcid.org/0000-0002-0669-4141
Fabio Malcher-MirandaHasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany.ORCID http://orcid.org/0000-0002-6823-5995
Serghei MangulUniversity of Southern California, Los Angeles, CA, USA.
Vanessa R MarcelinoSydney Medical School, The University of Sydney, Sydney, Australia.
Camille MarchetUniversité Lille, CNRS, CRIStAL, Lille, France.
Pierre MarijonDepartment of Computer Science, Inria, University of Lille, CNRS, Lille, France.
Dmitry MeleshkoCenter for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia.
Daniel R MendeAmsterdam University Medical Center, Amsterdam, the Netherlands.
Alessio MilaneseDepartment of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland.ORCID http://orcid.org/0000-0002-7050-2239
Niranjan NagarajanGenome Institute of Singapore, A*STAR, Singapore, Singapore.ORCID http://orcid.org/0000-0003-0850-5604
Jakob NissenDTU Health Tech, Kongens, Lyngby, Denmark.
Sergey NurkGenome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Leonid OlikerLawrence Berkeley National Laboratory, Berkeley, CA, USA.
Lucas PaoliDepartment of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland.
Pierre PeterlongoUniv. Rennes, Inria, CNRS, IRISA, Rennes, France.
Vitor C PiroHasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany.ORCID http://orcid.org/0000-0003-1330-1286
Jacob S PorterUniversity of Virginia, Charlottesville, VA, USA.
Simon RasmussenNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0001-6323-9041
Evan R ReesUniversity of Wisconsin-Madison, Madison, WI, USA.ORCID http://orcid.org/0000-0001-8405-9760
Knut ReinertInstitute for Bioinformatics, FU Berlin, Berlin, Germany.
Bernhard RenardHasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany.ORCID http://orcid.org/0000-0003-4589-9809
Espen Mikal RobertsenThe Arctic University of Norway, Tromsø, Norway.
Gail L RosenDrexel University, Philadelphia, PA, USA.
Hans-Joachim RuscheweyhDepartment of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland.
Varuni SarwalUniversity of California, Los Angeles, Los Angeles, CA, USA.
Nicola SegataDepartment CIBIO, University of Trento, Trento, Italy.ORCID http://orcid.org/0000-0002-1583-5794
Enrico SeilerInstitute for Bioinformatics, FU Berlin, Berlin, Germany.
Lizhen ShiFlorida Polytechnic University, Lakeland, FL, USA.
Fengzhu SunQuantitative and Computational Biology Department, University of Southern California, Los Angeles, CA, USA.
Shinichi SunagawaDepartment of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland.ORCID http://orcid.org/0000-0003-3065-0314
Søren Johannes SørensenUniversity of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0001-6227-9906
Ashleigh ThomasDOE Joint Genome Institute, Berkeley, CA, USA.ORCID http://orcid.org/0000-0001-7422-5649
Chengxuan TongGenome Institute of Singapore, Singapore, Singapore.
Mirko TrajkovskiDepartment of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland.ORCID http://orcid.org/0000-0002-3152-9551
Julien TremblayEnergy, Mining and Environment, National Research Council Canada, Montreal, Quebec, Canada.
Gherman UritskiyPhase Genomics, Seattle, WA, USA.
Riccardo VicedominiInstitut Pasteur, Paris, France.ORCID http://orcid.org/0000-0002-7706-0998
Zhengyang WangSchool of Computer Science, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0003-0118-1010
Ziye WangSchool of Mathematical Sciences, Fudan University, Shanghai, China.
Zhong WangDepartment of Energy Joint Genome Institute, Berkeley, CA, USA.
Andrew WarrenUniversity of Virginia, Charlottesville, VA, USA.
Nils Peder WillassenThe Arctic University of Norway, Tromsø, Norway.
Katherine YelickLawrence Berkeley National Laboratory, Berkeley, CA, USA.
Ronghui YouSchool of Computer Science, Fudan University, Shanghai, China.
Georg ZellerStructural and Computational Biology Unit, EMBL, Heidelberg, Germany.ORCID http://orcid.org/0000-0003-1429-7485
Zhengqiao ZhaoDrexel University, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0001-6873-6098
Shanfeng ZhuInstitute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.
Jie ZhuBGI-Shenzhen, Shenzhen, China.ORCID http://orcid.org/0000-0002-5789-6296
Ruben Garrido-OterMax Planck Institute for Plant Breeding Research, Köln, Germany.ORCID http://orcid.org/0000-0003-1769-892X
Petra GastmeierCharité-Universitätsmedizin Berlin, Berlin, Germany.
Stephane HacquardMax Planck Institute for Plant Breeding Research, Köln, Germany.ORCID http://orcid.org/0000-0003-2293-3525
Susanne HäußlerHelmholtz Centre for Infection Research, Braunschweig, Germany.ORCID http://orcid.org/0000-0001-6141-9102
Ariane KhalediHelmholtz Centre for Infection Research, Braunschweig, Germany.
Friederike MaechlerCharité-Universitätsmedizin Berlin, Berlin, Germany.
Fantin MesnyMax Planck Institute for Plant Breeding Research, Köln, Germany.ORCID http://orcid.org/0000-0002-3044-1398
Simona RadutoiuAarhus University, Aarhus, Denmark.
Paul Schulze-LefertMax Planck Institute for Plant Breeding Research, Köln, Germany.ORCID http://orcid.org/0000-0002-8978-1717
Nathiana SmitHelmholtz Centre for Infection Research, Braunschweig, Germany.
Till StrowigHelmholtz Centre for Infection Research, Braunschweig, Germany.
Andreas BremgesComputational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.
Alexander SczyrbaCenter for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.ORCID http://orcid.org/0000-0002-4405-3847
Alice Carolyn McHardyComputational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany. amc14@helmholtz-hzi.de.ORCID http://orcid.org/0000-0003-2370-3430
Funding
No grant is acknowledged in the PubMed record.
Abstract
Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses.
Indexed as
MetagenomeMetagenomicsArchaeaReproducibility of ResultsSequence Analysis, DNASoftware
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