ArticleFrontiers in microbiology2016
HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts.
Article in Frontiers in microbiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- The chromosomal genome sequence of the sponge,Wellcome open research · 2026Article
- Phage-induced disturbance of a marine sponge microbiome.Environmental microbiome · 2024Article
- Hecatomb: an integrated software platform for viral metagenomics.GigaScience · 2024Article
- The compact genome of the sponge Oopsacas minuta (Hexactinellida) is lacking key metazoan core genes.BMC biology · 2023Article
- Viral spillover risk increases with climate change in High Arctic lake sediments.Proceedings. Biological sciences · 2022Article
- Development and Validation of a Bioinformatic Workflow for the Rapid Detection of Viruses in Biosecurity.Viruses · 2022Article
- Symbiont transmission in marine sponges: reproduction, development, and metamorphosis.BMC biology · 2022Review
- Metagenomic Assessment of DNA Viral Diversity in Freshwater Sponges,Microorganisms · 2022Article
- Transmission studies and the composition of prokaryotic communities associated with healthy and diseased Aplysina cauliformis sponges suggest that Aplysina Red Band Syndrome is a prokaryotic polymicrobial disease.FEMS microbiology ecology · 2022Article
- Revisiting the rules of life for viruses of microorganisms.Nature reviews. Microbiology · 2021Review
- MultiPhATE2: code for functional annotation and comparison of phage genomes.G3 (Bethesda, Md.) · 2021Article
- Taxonomic, functional and expression analysis of viral communities associated with marine sponges.PeerJ · 2021Article
- Viral ecogenomics across the Porifera.Microbiome · 2020Article
- A hybrid pipeline for reconstruction and analysis of viral genomes at multi-organ level.GigaScience · 2020Article
- Metavirome datasets from two endemic Baikal spongesData in brief · 2020Article
- dsRNA-seq Reveals Novel RNA Virus and Virus-Like Putative Complete Genome Sequences from Hymeniacidon sp. Sponge.Microbes and environments · 2020Article
- Coral-Associated Viral Assemblages From the Central Red Sea Align With Host Species and Contribute to Holobiont Genetic Diversity.Frontiers in microbiology · 2020Article
- The Promises and Pitfalls of Machine Learning for Detecting Viruses in Aquatic Metagenomes.Frontiers in microbiology · 2019Article
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Authors and funding
8 authors.
Funding
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Abstract
Abundant 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.
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