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dc.contributor.authorLaffy, PW
dc.contributor.authorWood-Charlson, EM
dc.contributor.authorTuraev, D
dc.contributor.authorWeynberg, KD
dc.contributor.authorBotte, ES
dc.contributor.authorvan Oppen, MJH
dc.contributor.authorWebster, NS
dc.contributor.authorRattei, T
dc.date.accessioned2021-02-05T00:37:12Z
dc.date.available2021-02-05T00:37:12Z
dc.date.issued2016-06-09
dc.identifier.citationLaffy, P. W., Wood-Charlson, E. M., Turaev, D., Weynberg, K. D., Botte, E. S., van Oppen, M. J. H., Webster, N. S. & Rattei, T. (2016). HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts. FRONTIERS IN MICROBIOLOGY, 7 (JUN), https://doi.org/10.3389/fmicb.2016.00822.
dc.identifier.issn1664-302X
dc.identifier.urihttp://hdl.handle.net/11343/260080
dc.description.abstractAbundant bioinformatics resources are available for the study of complex microbial metagenomes, however their utility in viral metagenomics is limited. HoloVir is a robust and flexible data analysis pipeline that provides an optimized and validated workflow for taxonomic and functional characterization of viral metagenomes derived from invertebrate holobionts. Simulated viral metagenomes comprising varying levels of viral diversity and abundance were used to determine the optimal assembly and gene prediction strategy, and multiple sequence assembly methods and gene prediction tools were tested in order to optimize our analysis workflow. HoloVir performs pairwise comparisons of single read and predicted gene datasets against the viral RefSeq database to assign taxonomy and additional comparison to phage-specific and cellular markers is undertaken to support the taxonomic assignments and identify potential cellular contamination. Broad functional classification of the predicted genes is provided by assignment of COG microbial functional category classifications using EggNOG and higher resolution functional analysis is achieved by searching for enrichment of specific Swiss-Prot keywords within the viral metagenome. Application of HoloVir to viral metagenomes from the coral Pocillopora damicornis and the sponge Rhopaloeides odorabile demonstrated that HoloVir provides a valuable tool to characterize holobiont viral communities across species, environments, or experiments.
dc.languageEnglish
dc.publisherFRONTIERS MEDIA SA
dc.rights.urihttps://creativecommons.org/licenses/by/4.0
dc.titleHoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts
dc.typeJournal Article
dc.identifier.doi10.3389/fmicb.2016.00822
melbourne.affiliation.departmentSchool of BioSciences
melbourne.affiliation.facultyScience
melbourne.source.titleFrontiers in Microbiology
melbourne.source.volume7
melbourne.source.issueJUN
dc.rights.licenseCC BY
melbourne.elementsid1090448
melbourne.contributor.authorvan Oppen, Madeleine
dc.identifier.eissn1664-302X
melbourne.accessrightsOpen Access


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