ArticleScientific reports2013
Empirical validation of viral quasispecies assembly algorithms: state-of-the-art and challenges.
Article in Scientific reports, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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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
25 citing papers in PubMed.
- Trial
- Article
- Article
- PIQMEE: Bayesian Phylodynamic Method for Analysis of Large Data Sets with Duplicate Sequences.Molecular biology and evolution · 2020Article
- 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
- Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses.Viruses · 2020Article
- Porcine circovirus 2 (PCV-2) genetic variability under natural infection scenario reveals a complex network of viral quasispecies.Scientific reports · 2018Article
- geno2pheno[ngs-freq]: a genotypic interpretation system for identifying viral drug resistance using next-generation sequencing data.Nucleic acids research · 2018Article
- Towards Personalized Medicine: An ImprovedBioinformation · 2018Article
- Separation and assembly of deep sequencing data into discrete sub-population genomes.Nucleic acids research · 2017Article
- Invertebrate RNA virus diversity from a taxonomic point of view.Journal of invertebrate pathology · 2017Review
- De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline.BMC bioinformatics · 2017Article
- Challenges in the analysis of viral metagenomes.Virus evolution · 2016Review
- Distinguishing highly similar gene isoforms with a clustering-based bioinformatics analysis of PacBio single-molecule long reads.BioData mining · 2016Article
- Towards Better Precision Medicine: PacBio Single-Molecule Long Reads Resolve the Interpretation of HIV Drug Resistant Mutation Profiles at Explicit Quasispecies (Haplotype) Level.Journal of data mining in genomics & proteomics · 2016Article
- CoVaMa: Co-Variation Mapper for disequilibrium analysis of mutant loci in viral populations using next-generation sequence data.Methods (San Diego, Calif.) · 2015Article
- Estimation of evolutionary parameters using short, random and partial sequences from mixed samples of anonymous individuals.BMC bioinformatics · 2015Article
- Quasispecies Analyses of the HIV-1 Near-full-length Genome With Illumina MiSeq.Frontiers in microbiology · 2015Article
- RNA populations in immunocompromised patients as reservoirs for novel norovirus variants.Journal of virology · 2014Article
- Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations.Nucleic acids research · 2014Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Next generation sequencing (NGS) is superseding Sanger technology for analysing intra-host viral populations, in terms of genome length and resolution. We introduce two new empirical validation data sets and test the available viral population assembly software. Two intra-host viral population 'quasispecies' samples (type-1 human immunodeficiency and hepatitis C virus) were Sanger-sequenced, and plasmid clone mixtures at controlled proportions were shotgun-sequenced using Roche's 454 sequencing platform. The performance of different assemblers was compared in terms of phylogenetic clustering and recombination with the Sanger clones. Phylogenetic clustering showed that all assemblers captured a proportion of the most divergent lineages, but none were able to provide a high precision/recall tradeoff. Estimated variant frequencies mildly correlated with the original. Given the limitations of currently available algorithms identified by our empirical validation, the development and exploitation of additional data sets is needed, in order to establish an efficient framework for viral population reconstruction using NGS.
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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.