VIRE

VIRE — Viral Integrated Resource across Ecosystems — is a planetary-scale resource of viral genomes recovered from over 100,000 publicly available metagenomes spanning host-associated, aquatic, terrestrial, and anthropogenic environments. Using a unified pipeline, we identified 1.7 million high- and medium-quality viral genomes and annotated over 89 million predicted genes with functional, taxonomic, and host information. VIRE is integrated with SPIRE and MetaLog, enabling seamless links to bacterial/archaeal MAGs and curated environmental or clinical metadata from the same samples.

Cite VIRE

If you use VIRE in your research, please cite:

Nishijima S, Fullam A, Schmidt TSB, Kuhn M, Bork P.
VIRE: a metagenome-derived, planetary-scale virome resource with environmental context.
Nucleic Acids Research, 2026, Vol. 54, D1: D902–D911.
https://doi.org/10.1093/nar/gkaf1225

Contributors

Suguru Nishijima

European Molecular Biology Laboratory, Heidelberg
Life Science Data Research Center, University of Tokyo

Anthony Fullam

European Molecular Biology Laboratory, Heidelberg

Thomas S. B. Schmidt

European Molecular Biology Laboratory, Heidelberg
University College Cork

Michael Kuhn

European Molecular Biology Laboratory, Heidelberg

Peer Bork

European Molecular Biology Laboratory, Heidelberg
University of Würzburg
Max Delbrück Centre, Berlin

Bork Group @ EMBL — Molecular Systems Biology Unit, EMBL Heidelberg
Contribute — Report missing studies or data issues

Tools Used to Build VIRE

geNomad

Virus identification

CheckV

Genome QC

prodigal-gv

Gene calling

BACPHLIP

Lifestyle prediction

barrnap

rRNA prediction

fetchMGs

Marker gene extraction

NCBI BLAST+

Sequence search

megahit

Assembly

seqtk

Sequence processing

ngless

QC & preprocessing

Nextflow

Workflow management

Related Resources

SPIRE
Schmidt TSB, Fullam A, Ferretti P, Orakov A, Maistrenko OM, Ruscheweyh HJ, Letunic I, Duan Y, Van Rossum T, Sunagawa S, Mende DR, Finn RD, Kuhn M, Coelho LP, Bork P.
SPIRE: a Searchable, Planetary-scale mIcrobiome REsource.
Nucleic Acids Research, 2024, Vol. 52, D1: D777–D783.
https://doi.org/10.1093/nar/gkad943

MetaLog
Kuhn M, Schmidt TSB, Ferretti P, Głazek A, Robbani SM, Akanni W, Fullam A, Schudoma C, Cetin E, Hassan M, Noack K, Schwarz A, Thielemann R, Thomas L, von Stetten M, Alves R, Iyappan A, Kartal E, Kel I, Keller MI, Maistrenko O, Mankowski A, Nishijima S, Podlesny D, Schiller J, Schulz S, Van Rossum T, Bork P.
Metalog: curated and harmonised contextual data for global metagenomics samples.
Nucleic Acids Research, 2026, Vol. 54, D1: D826–D834.
https://doi.org/10.1093/nar/gkaf1118

proGenomes
Fullam A, Letunic I, Maistrenko OM, Castro AA, Coelho LP, Grekova A, Schudoma C, Khedkar S, Robbani M, Kuhn M, Schmidt TSB, Bork P, Mende DR.
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes.
Nucleic Acids Research, 2026, Vol. 54, D1: D852–D857.
https://doi.org/10.1093/nar/gkaf1208

metaTraits
Podlesny D, Kim CY, Robbani SM, Schudoma C, Fullam A, Reimer LC, Koblitz J, Schober I, Iyappan A, Van Rossum T, Schiller J, Grekova A, Kuhn M, Bork P.
metaTraits: a large-scale integration of microbial phenotypic trait information.
Nucleic Acids Research, 2026, Vol. 54, D1: D835–D841.
https://doi.org/10.1093/nar/gkaf1241

GMGC
Coelho LP, Alves R, del Río ÁR, Myers PN, Cantalapiedra CP, Giner-Lamia J, Schmidt TS, Mende DR, Orakov A, Letunic I, Hildebrand F, Van Rossum T, Forslund SK, Khedkar S, Maistrenko OM, Pan S, Jia L, Ferretti P, Sunagawa S, Zhao XM, Nielsen HB, Huerta-Cepas J, Bork P.
Towards the biogeography of prokaryotic genes.
Nature, 2021, Vol. 601, Issue 7892: 252–256.
https://doi.org/10.1038/s41586-021-04233-4

EggNOG
Hernández-Plaza A, Szklarczyk D, Botas J, Cantalapiedra CP, Giner-Lamia J, Mende DR, Kirsch R, Rattei T, Letunic I, Jensen LJ, Bork P, von Mering C, Huerta-Cepas J.
eggNOG 6.0: enabling comparative genomics across 12 535 organisms.
Nucleic Acids Research, 2023, Vol. 51, D1: D389–D394.
https://doi.org/10.1093/nar/gkac1022