ArticlemBio2014
Standards for sequencing viral genomes in the era of high-throughput sequencing.
Article in mBio, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 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
65 citing papers in PubMed, 157 citations in OpenAlex.
- Genomic characterization and phylogenetic placement of Matryoshka RNA virus 1 associated with Plasmodium vivax malaria in Africa.Access microbiology · 2026Article
- 'PePApipe': A complete bioinformatics analysis pipeline for African Swine Fever Virus genome.PloS one · 2026Article
- Epidemiological surveillance and phylogenetic diversity of Orthohantavirus hantanense using high-fidelity nanopore sequencing, Republic of Korea.PLoS neglected tropical diseases · 2025Article
- Experimental evidence of vaccine-driven evolution of respiratory syndrome virus type 2.Virus evolution · 2025Article
- Improving the reporting of metagenomic virome-scale data.Communications biology · 2024Article
- Monkeypox virus genomic accordion strategies.Nature communications · 2024Article
- Detection of dengue virus serotype 4 in Panama after 23 years without circulation.Frontiers in cellular and infection microbiology · 2024Article
- Ten common issues with reference sequence databases and how to mitigate them.Frontiers in bioinformatics · 2024Review
- An amplicon-based protocol for whole-genome sequencing of human respiratory syncytial virus subgroup A.Biology methods & protocols · 2024Article
- A Development of Rapid Whole-Genome Sequencing ofViruses · 2023Article
- Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification.Nature biotechnology · 2023Article
- Pending Reorganization ofViruses · 2023Article
- Four principles to establish a universal virus taxonomy.PLoS biology · 2023Article
- SARS-CoV-2 Infections in Vaccinated and Unvaccinated Populations in Camp Lemonnier, Djibouti, from April 2020 to January 2022.Viruses · 2022Article
- Metatranscriptomics to characterize respiratory virome, microbiome, and host response directly from clinical samples.Cell reports methods · 2021Article
- Article
- Identification of a novel filovirus in a common lancehead (Bothrops atrox (Linnaeus, 1758)).The Journal of veterinary medical science · 2021Article
- Article
- Genomic characterization of 99 viruses from the bunyavirus families Nairoviridae, Peribunyaviridae, and Phenuiviridae, including 35 previously unsequenced viruses.PLoS pathogens · 2021Article
- Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives.Frontiers in microbiology · 2021Review
5 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
- Commented on by
Authors and funding
17 authors at 9 institutions in 1 country.
Funding
Abstract
Thanks to high-throughput sequencing technologies, genome sequencing has become a common component in nearly all aspects of viral research; thus, we are experiencing an explosion in both the number of available genome sequences and the number of institutions producing such data. However, there are currently no common standards used to convey the quality, and therefore utility, of these various genome sequences. Here, we propose five "standard" categories that encompass all stages of viral genome finishing, and we define them using simple criteria that are agnostic to the technology used for sequencing. We also provide genome finishing recommendations for various downstream applications, keeping in mind the cost-benefit trade-offs associated with different levels of finishing. Our goal is to define a common vocabulary that will allow comparison of genome quality across different research groups, sequencing platforms, and assembly techniques.
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.