VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

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dc.contributor.authorGuo, Jiarong
dc.contributor.authorBolduc, Ben
dc.contributor.authorZayed, Ahmed A
dc.contributor.authorVarsani, Arvind
dc.contributor.authorDominguez-Huerta, Guillermo
dc.contributor.authorDelmont, Tom O
dc.contributor.authorPratama, Akbar A
dc.contributor.authorGazitúa, M. C
dc.contributor.authorVik, Dean
dc.contributor.authorSullivan, Matthew B
dc.contributor.authorRoux, Simon
dc.date.accessioned2021-10-12T09:29:36Z
dc.date.available2021-10-12T09:29:36Z
dc.date.issued2021-02-01
dc.date.updated2021-02-07T04:12:59Z
dc.description.abstractBackground 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 ). Video abstracten_US
dc.identifier.apacitationGuo, J., Bolduc, B., Zayed, A. A., Varsani, A., Dominguez-Huerta, G., Delmont, T. O., ... Roux, S. (2021). VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. <i>Microbiome</i>, 9(Article number: 37), http://hdl.handle.net/11427/35194en_ZA
dc.identifier.chicagocitationGuo, Jiarong, Ben Bolduc, Ahmed A Zayed, Arvind Varsani, Guillermo Dominguez-Huerta, Tom O Delmont, Akbar A Pratama, et al "VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses." <i>Microbiome</i> 9, Article number: 37. (2021) http://hdl.handle.net/11427/35194en_ZA
dc.identifier.citationGuo, J., Bolduc, B., Zayed, A.A., Varsani, A., Dominguez-Huerta, G., Delmont, T.O., Pratama, A.A. & Gazitúa, M. C. et al. 2021. VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. <i>Microbiome.</i> 9(Article number: 37) http://hdl.handle.net/11427/35194en_ZA
dc.identifier.ris TY - Journal Article AU - Guo, Jiarong AU - Bolduc, Ben AU - Zayed, Ahmed A AU - Varsani, Arvind AU - Dominguez-Huerta, Guillermo AU - Delmont, Tom O AU - Pratama, Akbar A AU - Gazitúa, M. C AU - Vik, Dean AU - Sullivan, Matthew B AU - Roux, Simon AB - 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 ). Video abstract DA - 2021-02-01 DB - OpenUCT DP - University of Cape Town IS - Article number: 37 J1 - Microbiome LK - https://open.uct.ac.za PY - 2021 T1 - VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses TI - VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses UR - http://hdl.handle.net/11427/35194 ER - en_ZA
dc.identifier.urihttps://doi.org/10.1186/s40168-020-00990-y
dc.identifier.urihttp://hdl.handle.net/11427/35194
dc.identifier.vancouvercitationGuo J, Bolduc B, Zayed AA, Varsani A, Dominguez-Huerta G, Delmont TO, et al. VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome. 2021;9(Article number: 37) http://hdl.handle.net/11427/35194.en_ZA
dc.language.isoenen_US
dc.language.rfc3066en
dc.publisher.departmentDepartment of Integrative Biomedical Sciencesen_US
dc.publisher.facultyFaculty of Health Sciencesen_US
dc.rights.holderThe Author(s)
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_US
dc.rights.urihttps://microbiomejournal.biomedcentral.com/
dc.sourceMicrobiomeen_US
dc.source.journalissueArticle number: 37en_US
dc.source.journalvolume9en_US
dc.source.urihttps://microbiomejournal.biomedcentral.com/
dc.titleVirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA virusesen_US
dc.typeJournal Articleen_US
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