Identification of mobile genetic elements with geNomad

Camargo, Antonio Pedro; Roux, Simon; Schulz, Frederik; Babinski, Michal; Xu, Yan; Hu, Bin; Chain, Patrick S. G.; Nayfach, Stephen; Kyrpides, Nikos C.

doi:10.1038/s41587-023-01953-y

Title: Identification of mobile genetic elements with geNomad

Journal Article · 20 September 2023 · Nature Biotechnology

DOI: https://doi.org/10.1038/s41587-023-01953-y · OSTI ID:2280932

^[1]; Roux, Simon ^[1];

^[1]; Babinski, Michal ^[2];

^[2]; Hu, Bin ^[2];

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Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Identifying and characterizing mobile genetic elements in sequencing data is essential for understanding their diversity, ecology, biotechnological applications and impact on public health. Here we introduce geNomad, a classification and annotation framework that combines information from gene content and a deep neural network to identify sequences of plasmids and viruses. geNomad uses a dataset of more than 200,000 marker protein profiles to provide functional gene annotation and taxonomic assignment of viral genomes. Using a conditional random field model, geNomad also detects proviruses integrated into host genomes with high precision. In benchmarks, geNomad achieved high classification performance for diverse plasmids and viruses (Matthews correlation coefficient of 77.8% and 95.3%, respectively), substantially outperforming other tools. Leveraging geNomad’s speed and scalability, we processed over 2.7 trillion base pairs of sequencing data, leading to the discovery of millions of viruses and plasmids that are available through the IMG/VR and IMG/PR databases. geNomad is available at https://portal.nersc.gov/genomad.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science (BSS); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); USDOE National Nuclear Security Administration (NNSA)

Grant/Contract Number:: AC02-05CH11231; 89233218CNA000001; AC05-00OR22725; AC05-76RL01830

OSTI ID:: 2280932

Journal Information:: Nature Biotechnology, Journal Name: Nature Biotechnology Vol. 42; ISSN 1087-0156

Publisher:: Springer NatureCopyright Statement

Country of Publication:: United States

Language:: English

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Title: Identification of mobile genetic elements with geNomad

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