ArticlePloS one2012
Read length versus depth of coverage for viral quasispecies reconstruction.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
36 citing papers in PubMed.
- Trial
- Comparison of illumina and 454 deep sequencing in participants failing raltegravir-based antiretroviral therapy.PloS one · 2014Trial
- QoALa: A comprehensive workflow for viral quasispecies diversity comparison using long-read sequencing data.PLoS computational biology · 2026Article
- Setu: a pipeline for the robust assembly of SARS-CoV-2 genomes.Microbiology resource announcements · 2024Article
- Influence of Environmental Factors and Genome Diversity on Cumulative COVID-19 Cases in the Highland Region of China: Comparative Correlational Study.Interactive journal of medical research · 2024Article
- Evolutionary Analysis of Pre-S/S Mutations in HBeAg-Negative Chronic Hepatitis B With HBsAg < 100 IU/ml.Frontiers in public health · 2021Article
- Article
- Inter- Versus Intra-Host Sequence Diversity of pH1N1 and Associated Clinical Outcomes.Microorganisms · 2020Article
- A proofreading-impaired herpesvirus generates populations with quasispecies-like structure.Nature microbiology · 2019Article
- Genomic characterization of hepatitis C virus transmitted founder variants with deep sequencing.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2019Article
- A high-throughput SNP discovery strategy for RNA-seq data.BMC genomics · 2019Article
- Link between the numbers of particles and variants founding new HIV-1 infections depends on the timing of transmission.Virus evolution · 2019Article
- SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution.GigaScience · 2018Article
- Separation and assembly of deep sequencing data into discrete sub-population genomes.Nucleic acids research · 2017Article
- Comparison of error correction algorithms for Ion Torrent PGM data: application to hepatitis B virus.Scientific reports · 2017Article
- De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline.BMC bioinformatics · 2017Article
- Evolution of full-length genomes of HBV quasispecies in sera of patients with a coexistence of HBsAg and anti-HBs antibodies.Scientific reports · 2017Article
- Software Dedicated to Virus Sequence Analysis "Bioinformatics Goes Viral".Advances in virus research · 2017Article
- Genotyping assay for differentiation of wild-type and vaccine viruses in subjects immunized with live attenuated influenza vaccine.PloS one · 2017Article
- Detection of Natural Resistance-Associated Substitutions by Ion Semiconductor Technology in HCV1b Positive, Direct-Acting Antiviral Agents-Naïve Patients.International journal of molecular sciences · 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
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent advancements of sequencing technology have opened up unprecedented opportunities in many application areas. Virus samples can now be sequenced efficiently with very deep coverage to infer the genetic diversity of the underlying virus populations. Several sequencing platforms with different underlying technologies and performance characteristics are available for viral diversity studies. Here, we investigate how the differences between two common platforms provided by 454/Roche and Illumina affect viral diversity estimation and the reconstruction of viral haplotypes. Using a mixture of ten HIV clones sequenced with both platforms and additional simulation experiments, we assessed the trade-off between sequencing coverage, read length, and error rate. For fixed costs, short Illumina reads can be generated at higher coverage and allow for detecting variants at lower frequencies. They can also be sufficient to assess the diversity of the sample if sequences are dissimilar enough, but, in general, assembly of full-length haplotypes is feasible only with the longer 454/Roche reads. The quantitative comparison highlights the advantages and disadvantages of both platforms and provides guidance for the design of viral diversity studies.
Indexed as
Identifiers
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.