ArticleBriefings in bioinformatics2023
VIGA: a one-stop tool for eukaryotic virus identification and genome assembly from next-generation-sequencing data.
Article in Briefings in bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 6 citations in OpenAlex.
- Genomic characterization of Mycoplasma bovis, Mannheimia haemolytica, and bovine viral diarrhea virus 1 from a bovine respiratory disease complex case.BMC genomic data · 2026Article
- Invertebrate Iridescent Viruses (Viruses · 2025Article
- Choosing the most suitable NGS technology to combine with a standardized viral enrichment protocol for obtaining complete avian orthoreovirus genomes from metagenomic samples.Frontiers in bioinformatics · 2025Article
- Improving the reporting of metagenomic virome-scale data.Communications biology · 2024Article
- Ten computational challenges in human virome studies.Virologica Sinica · 2024Review
- An updated database of virus circular RNAs provides new insights into the biogenesis mechanism of the molecule.Emerging microbes & infections · 2023Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Identification of viruses and further assembly of viral genomes from the next-generation-sequencing data are essential steps in virome studies. This study presented a one-stop tool named VIGA (available at https://github.com/viralInformatics/VIGA) for eukaryotic virus identification and genome assembly from NGS data. It was composed of four modules, namely, identification, taxonomic annotation, assembly and novel virus discovery, which integrated several third-party tools such as BLAST, Trinity, MetaCompass and RagTag. Evaluation on multiple simulated and real virome datasets showed that VIGA assembled more complete virus genomes than its competitors on both the metatranscriptomic and metagenomic data and performed well in assembling virus genomes at the strain level. Finally, VIGA was used to investigate the virome in metatranscriptomic data from the Human Microbiome Project and revealed different composition and positive rate of viromes in diseases of prediabetes, Crohn's disease and ulcerative colitis. Overall, VIGA would help much in identification and characterization of viromes, especially the known viruses, in future studies.
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Registered trials
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