geNomad

geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes.

Speed

geNomad is significantly faster than similar tools and can be used to process large datasets.

Taxonomic assignment

The identified viruses are assigned to taxonomic lineages that follow the latest ICTV taxonomy release.

Functional annotation

Genes encoded by viruses and plasmids are functionally annotated using geNomad’s marker database.

Get started

To start using geNomad, read the installation and quickstart guides below. In case you want to learn more details about how geNomad works, visit the pages listed in the sidebar.

Installation

Instructions on how to install geNomad in your computer or server.

Quickstart

Learn how to run geNomad and interpret its results.

Web app

geNomad is also available as a web app in the NMDC EDGE platform. There you can upload your sequence data, visualize the results in your browser, and download the data to your computer.

Citing geNomad

If you use geNomad in your work, please consider citing its manuscript:

Identification of mobile genetic elements with geNomad Camargo, A. P., Roux, S., Schulz, F., Babinski, M., Xu, Y., Hu, B., Chain, P. S. G., Nayfach, S., & Kyrpides, N. C. — Nature Biotechnology (2023), DOI: 10.1038/s41587-023-01953-y.

Ask a question or report a bug

If you want to ask a question about geNomad or report a problem you had with it, please create an issue in the GitHub repository.