ArticleBioinformatics (Oxford, England)2014
Accurate viral population assembly from ultra-deep sequencing data.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
23 citing papers in PubMed, 61 citations in OpenAlex.
- Algorithms for Short-Read Viral Haplotype Reconstruction: Challenges, Solutions, and Perspectives.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Embracing Complexity: What Novel Sequencing Methods Are Teaching Us About Herpesvirus Genomic Diversity.Annual review of virology · 2024Review
- Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction.Nucleic acids research · 2021Article
- Epidemiological data analysis of viral quasispecies in the next-generation sequencing era.Briefings in bioinformatics · 2021Review
- Alphaherpesvirus Genomics: Past, Present and Future.Current issues in molecular biology · 2021Review
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- Evaluation of haplotype callers for next-generation sequencing of viruses.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2020Article
- Article
- Mutational pathway maps and founder effects define the within-host spectrum of hepatitis C virus mutants resistant to drugs.PLoS pathogens · 2019Article
- Estimating HIV-1 Genetic Diversity in Brazil Through Next-Generation Sequencing.Frontiers in microbiology · 2019Article
- Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons.PLoS computational biology · 2018Article
- Laboratory Methods in Molecular Epidemiology: Viral Infections.Microbiology spectrum · 2018Review
- Viral quasispecies reconstruction via tensor factorization with successive read removal.Bioinformatics (Oxford, England) · 2018Article
- Separation and assembly of deep sequencing data into discrete sub-population genomes.Nucleic acids research · 2017Article
- Six Highly Conserved Targets of RNAi Revealed in HIV-1-Infected Patients from Russia Are Also Present in Many HIV-1 Strains Worldwide.Molecular therapy. Nucleic acids · 2017Article
- Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants.Journal of computational biology : a journal of computational molecular cell biology · 2017Article
- De novo assembly of viral quasispecies using overlap graphs.Genome research · 2017Article
- A random forest classifier for detecting rare variants in NGS data from viral populations.Computational and structural biotechnology journal · 2017Article
- Estimation of genetic diversity in viral populations from next generation sequencing data with extremely deep coverage.Algorithms for molecular biology : AMB · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
motivationNext-generation sequencing technologies sequence viruses with ultra-deep coverage, thus promising to revolutionize our understanding of the underlying diversity of viral populations. While the sequencing coverage is high enough that even rare viral variants are sequenced, the presence of sequencing errors makes it difficult to distinguish between rare variants and sequencing errors.
resultsIn this article, we present a method to overcome the limitations of sequencing technologies and assemble a diverse viral population that allows for the detection of previously undiscovered rare variants. The proposed method consists of a high-fidelity sequencing protocol and an accurate viral population assembly method, referred to as Viral Genome Assembler (VGA). The proposed protocol is able to eliminate sequencing errors by using individual barcodes attached to the sequencing fragments. Highly accurate data in combination with deep coverage allow VGA to assemble rare variants. VGA uses an expectation-maximization algorithm to estimate abundances of the assembled viral variants in the population. RESULTS on both synthetic and real datasets show that our method is able to accurately assemble an HIV viral population and detect rare variants previously undetectable due to sequencing errors. VGA outperforms state-of-the-art methods for genome-wide viral assembly. Furthermore, our method is the first viral assembly method that scales to millions of sequencing reads. AVAILABILITY: Our tool VGA is freely available at http://genetics.cs.ucla.edu/vga/
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What OpenQuestion holds
Registered trials
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.