ArticleRNA (New York, N.Y.)2023
VODKA2: a fast and accurate method to detect non-standard viral genomes from large RNA-seq data sets.
Article in RNA (New York, N.Y.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 18 citations in OpenAlex.
- Identification of fidelity-determined residues of Porcine reproductive and respiratory syndrome virus through structural alignment.Virulence · 2026Article
- Accounting for Defective Viral Genomes in viral consensus genome reconstruction, application to influenza virus.PLoS computational biology · 2026Article
- Detailed single-cell mapping of the transcriptional response to a virus infection driven by copy-back viral genomes.PLoS pathogens · 2026Article
- Variable and conserved features of copy-back viral genome populations generatedJournal of virology · 2026Article
- Molecular characterization of arenavirus defective viral genomes reveals sequence features associated with their formation.Journal of virology · 2026Article
- Detailed single-cell mapping of the transcriptional response to a virus infection driven by copy-back viral genomes.bioRxiv : the preprint server for biology · 2026Article
- Classification, functions, evolution, and applications of defective viral genomes.Frontiers in microbiology · 2026Review
- Review
- Defective but promising: evaluating the utility of currently available bioinformatic pipelines for detecting defective viral genomes in RNA-Seq data.The Journal of general virology · 2025Article
- Validation of diverse and previously untraceable Sendai virus copyback viral genomes by direct RNA sequencing.Journal of virology · 2025Article
- Deletion viral genome diversity among bovine viral diarrhea virus (BVDV) 1a and 1b strains.Virology journal · 2025Article
- Review
- Validation of diverse and previously untraceable Sendai virus copyback viral genomes by Direct RNA Sequencing.bioRxiv : the preprint server for biology · 2025Article
- Bovine viral diarrhea virus 2 strains generate deletion viral genomes primarily in the NS2 region of the viral genome.Frontiers in veterinary science · 2025Article
- Quantifying defective and wild-type viruses from high-throughput RNA sequencing.Bioinformatics (Oxford, England) · 2024Article
- S RNA Intergenic Deletions Drive Viral Interference during Arenavirus Infections.bioRxiv : the preprint server for biology · 2023Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
During viral replication, viruses carrying an RNA genome produce non-standard viral genomes (nsVGs), including copy-back viral genomes (cbVGs) and deletion viral genomes (delVGs), that play a crucial role in regulating viral replication and pathogenesis. Because of their critical roles in determining the outcome of RNA virus infections, the study of nsVGs has flourished in recent years, exposing a need for bioinformatic tools that can accurately identify them within next-generation sequencing data obtained from infected samples. Here, we present our data analysis pipeline, Viral Opensource DVG Key Algorithm 2 (VODKA2), that is optimized to run on a parallel computing environment for fast and accurate detection of nsVGs from large data sets.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.