Skip to main content
SpringerLink
Log in

Fast and accurate identification of plasmids and viruses in sequencing data using geNomad

  • Research Briefing
  • Published:

From Nature Biotechnology

View current issue Submit your manuscript

The detection of mobile genetic elements is crucial for exploring the ecology and evolution of microbial communities, and it has diverse implications in biotechnology and public health. geNomad is a computational framework that enables researchers to precisely identifiy and annotate plasmids and viruses in sequencing data on a large scale.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1: geNomad framework for identifying and annotating viruses and plasmids.

References

  1. Koonin, E. V. Viruses and mobile elements as drivers of evolutionary transitions. Phil. Trans. R. Soc. B 371, 20150442 (2016). A review that discusses how MGEs function as genetic reservoirs that allow major evolutionary transitions.

    Article  PubMed  PubMed Central  Google Scholar 

  2. Durrant, M. G. et al. Systematic discovery of recombinases for efficient integration of large DNA sequences into the human genome. Nat Biotechnol. 41, 488–499 (2023). This paper reports the discovery of thousands of MGE-encoded large serine integrases with recombination activity in human cells.

    Article  CAS  PubMed  Google Scholar 

  3. San Millan, A. Evolution of plasmid-mediated antibiotic resistance in the clinical context. Trends Microbiol. 26, 978–985 (2018). A review discussing the role of plasmids in the spread of antibiotic resistance genes in clinical settings.

    Article  CAS  PubMed  Google Scholar 

  4. Paez-Espino, D. et al. Uncovering Earth’s virome. Nature 536, 425–430 (2016). This paper identifies over a hundred thousand virus genomes in metagenomic sequencing data, expanding the number of known viral genes at that time by 16-fold.

    Article  CAS  PubMed  Google Scholar 

  5. Camargo, A. P. et al. IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata. Nuc. Acids Res. 51, D733–D743 (2023). This paper describes the IMG/VR v4 database, which was created using geNomad and includes more than 15 million sequences of viral genomes.

    Article  CAS  Google Scholar 

Download references

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

This is a summary of: Camargo, A. P. et al. Identification of mobile genetic elements with geNomad. Nat. Biotechnol. https://doi.org/10.1038/s41587-023-01953-y (2023).

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Fast and accurate identification of plasmids and viruses in sequencing data using geNomad. Nat Biotechnol (2023). https://doi.org/10.1038/s41587-023-01982-7

Download citation

  • Published:

  • DOI: https://doi.org/10.1038/s41587-023-01982-7

  • Springer Nature America, Inc.

Search

Navigation