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Antônio Pedro Camargo, Simon Roux, Frederik Schulz, Michal Babinski, Yan Xu, Bin Hu, Patrick Chain, Stephen Nayfach, Nikos C. Kyrpides
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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Camargo, A. P., Roux, S., Schulz, F., Babinski, M., Xu, Y., Hu, B., Chain, P., Nayfach, S., & Kyrpides, N. C. (2023). Identification of mobile genetic elements with geNomad. Nature Biotechnology, 42(8), 1303–1312. https://doi.org/10.1038/s41587-023-01953-y
Camargo, Antônio Pedro, et al. "Identification of mobile genetic elements with geNomad." Nature Biotechnology, vol. 42, no. 8, 2023, pp. 1303–1312, https://doi.org/10.1038/s41587-023-01953-y.
Camargo, Antônio Pedro, Simon Roux, Frederik Schulz, Michal Babinski, Yan Xu, Bin Hu, Patrick Chain, Stephen Nayfach, and Nikos C. Kyrpides. "Identification of mobile genetic elements with geNomad." Nature Biotechnology 42, no. 8 (2023): 1303–1312. https://doi.org/10.1038/s41587-023-01953-y.
Camargo A. P., Roux S., Schulz F. [и др.] Identification of mobile genetic elements with geNomad // Nature Biotechnology. — 2023. — Vol. 42, № 8. — P. 1303–1312. — URL: https://doi.org/10.1038/s41587-023-01953-y
@article{camargo2023identification,
title = {{Identification of mobile genetic elements with geNomad}},
author = {Antônio Pedro Camargo and Simon Roux and Frederik Schulz and Michal Babinski and Yan Xu and Bin Hu and Patrick Chain and Stephen Nayfach and Nikos C. Kyrpides},
journal = {Nature Biotechnology},
year = {2023},
volume = {42},
number = {8},
pages = {1303--1312},
doi = {10.1038/s41587-023-01953-y},
url = {https://doi.org/10.1038/s41587-023-01953-y}
}TY - JOUR AU - Camargo, Antônio Pedro AU - Roux, Simon AU - Schulz, Frederik AU - Babinski, Michal AU - Xu, Yan AU - Hu, Bin AU - Chain, Patrick AU - Nayfach, Stephen AU - Kyrpides, Nikos C. TI - Identification of mobile genetic elements with geNomad JO - Nature Biotechnology VL - 42 IS - 8 SP - 1303 EP - 1312 PY - 2023 DA - 2023/09/21 DO - 10.1038/s41587-023-01953-y UR - https://doi.org/10.1038/s41587-023-01953-y ER -
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