First community challenge for automated virus taxonomy

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Abstract
The rapid rate of virus discovery renders manual curation by taxonomy experts increasingly impractical, creating a need for reliable software that can reproducibly assign viral contigs to taxa at all fifteen ranks of the virus taxonomy. We led an open community challenge for the computational taxonomic classification of viruses and assembled a dataset of virus sequences combining expert-curated and metagenomic sequences. Seventeen teams contributed a total of thirty-four automated, fully reproducible classification pipelines. Most tools correctly assigned viruses belonging to established species, genera, or families, but viruses that are unclassified at those lower ranks remain challenging. This study provides datasets, open-source software, novel approaches, and recommendations to benchmark computational taxonomic classification of viruses, and support organizing the many viruses discovered in big omics data.
Funding Information
  • National Natural Science Foundation of China (32270019)
  • Pawsey Supercomputing Research Centre’s Setonix Supercomputer
  • National Center for Biotechnology Information of the National Library of Medicine (NLM), National Institutes of Health (5U01DE034196-02)
  • Fundação de Amparo à Pesquisa do Estado de São Paulo (2021/10577-0)
  • Fonds Wetenschappelijk Onderzoek (11L1325N)
  • National Science Centre, Poland (DEC-2022/45/B/ST6/03032)
  • European Research Council (865694)
  • European Research Council (955974)
  • European Research Council (101137311)
  • Deutsche Forschungsgemeinschaft (39071386)
  • Alexander von Humboldt-Stiftung
  • Australian Research Council (DP250103825)
  • Australian Research Council (FL250100019)
  • European Union, ViroInf (955974)
  • National Research Foundation of Korea (2020M3-A9G7-103933)
  • National Research Foundation of Korea (RS-2021-NR061659)
  • National Research Foundation of Korea (RS-2021-NR056571)
  • National Research Foundation of Korea (RS-2024-00396026)
  • Samsung DS research fund
  • Novo Nordisk Fonden (NNF24SA0092560)
  • UKRI Horizon Europe Guarantee Program (EP/Y029585/1)
  • National Institute of Allergy and Infectious Diseases (U24AI162625)
  • National Natural Science Foundation of China (32270019)
  • Vetenskapsrådet (2023-03310_VR)
  • Italian national Node (MIRRI-IT) of the European Research Infrastructure MIRRI-ERIC
  • Mississippi Agricultural and Forestry Experiment Station (58-6066-3-044)
  • USDA-NIFA SCRI
  • NIFA-USDA (7006130)
  • Innovation and Technology Commission - Hong Kong (MRP/071/20X)
  • he University of Melbourne’s Research Computing Services and the Petascale Campus Initiative
  • National Science Foundation (2412446)
  • Poznań Supercomputing and Networking Center (pl0074-02)
  • U.S. Department of Energy Joint Genome Institute (DE-AC02-05CH11231)

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