The DOI matches its Crossref record; 70 of the 70 references it cites were found in a registry or an index.
VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses
Open accessAbstract
Background: Viruses are a significant player in many biosphere and human ecosystems, but most signals remain “hidden” in metagenomic/metatranscriptomic sequence datasets due to the lack of universal gene markers, database representatives, and insufficiently advanced identification tools. Results: Here, we introduce VirSorter2, a DNA and RNA virus identification tool that leverages genome-informed database advances across a collection of customized automatic classifiers to improve the accuracy and range of virus sequence detection. When benchmarked against genomes from both isolated and uncultivated viruses, VirSorter2 uniquely performed consistently with high accuracy (F1-score > 0.8) across viral diversity, while all other tools under-detected viruses outside of the group most represented in reference databases (i.e., those in the order Caudovirales). Among the tools evaluated, VirSorter2 was also uniquely able to minimize errors associated with atypical cellular sequences including eukaryotic genomes and plasmids. Finally, as the virosphere exploration unravels novel viral sequences, VirSorter2’s modular design makes it inherently able to expand to new types of viruses via the design of new classifiers to maintain maximal sensitivity and specificity. Conclusion: With multi-classifier and modular design, VirSorter2 demonstrates higher overall accuracy across major viral groups and will advance our knowledge of virus evolution, diversity, and virus-microbe interaction in various ecosystems. Source code of VirSorter2 is freely available (https://bitbucket.org/MAVERICLab/virsorter2), and VirSorter2 is also available both on bioconda and as an iVirus app on CyVerse (https://de.cyverse.org/de).
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Life and death in the soil microbiome: how ecological processes influence biogeochemistry
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Self-citationIdentification 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. (2024) · Nature Biotechnology · doi:10.1038/s41587-023-01953-y · Cited by 980
Self-citationSystematic and quantitative view of the antiviral arsenal of prokaryotes
Tesson, F., Hervé, A., Mordret, E., Touchon, M., d’Humières, C., Cury, J., & Bernheim, A. (2022) · Nature Communications · doi:10.1038/s41467-022-30269-9 · Cited by 759
Petabase-scale sequence alignment catalyses viral discovery
Edgar, R. C., Taylor, B., Lin, V., Altman, T., Barbera, P., Meleshko, D., Lohr, D., Novakovsky, G., Buchfink, B., Al-Shayeb, B., et al. (2022) · Nature · doi:10.1038/s41586-021-04332-2 · Cited by 498
Metadata
- Authors
- Guo, J., Bolduc, B., Zayed, A. A., Varsani, A., Dominguez-Huerta, G., Delmont, T. O., Pratama, A. A., Gazitúa, M. C., Vik, D., Sullivan, M. B., & Roux, S.
- Venue
- Microbiome
- Published
- 2021-02-01
- Volume
- 9
- Issue
- 1
- Pages
- 37-37
- ISSN
- 2049-2618 (ISSN-L)
- OpenAlex
- W3127656915
- Cited by
- 1,279
- References
- 70
- FWCI
- 92.12
- Type
- journal article
- Language
- en
- Open access
- gold
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- Guo, J., Bolduc, B., Zayed, A. A., Varsani, A., Dominguez-Huerta, G., Delmont, T. O., Pratama, A. A., Gazitúa, M. C., Vik, D., Sullivan, M. B., & Roux, S. (2021). VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome. https://doi.org/10.1186/s40168-020-00990-y
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