ArticleGigaScience2024
V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation.
Article in GigaScience, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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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
11 citing papers in PubMed.
- metaWEPP: leveraging biobank-scale intra-species phylogenies for near-haplotype resolution in metagenomic analysis.NAR genomics and bioinformatics · 2026Article
- Distinct Host Gene Expression Patterns Induced by Covert Deformed Wing Virus Infections in Honeybees (Apis mellifera).Archives of insect biochemistry and physiology · 2026Article
- WEPP: Phylogenetic placement achieves near-haplotype resolution in wastewater-based epidemiology.PLoS computational biology · 2026Article
- Tracking SARS-CoV-2 genomic variants in wastewater sequencing data with LolliPop.PLoS computational biology · 2026Article
- A recurrent adaptive mutation in the transmembrane 2B protein of an insect picorna-like virus in a nonnative host.Journal of virology · 2026Article
- ViromeXplore: integrative workflows for complete and reproducible virome characterization.Briefings in bioinformatics · 2025Article
- Estimated transmission dynamics of SARS-CoV-2 variants from wastewater are unbiased and robust to differential shedding.Nature communications · 2025Article
- PathoSeq-QC: a decision support bioinformatics workflow for robust genomic surveillance.Bioinformatics (Oxford, England) · 2025Article
- Insights into diversity, host range, and evolution of iflaviruses in Lepidoptera through transcriptome mining.Virus evolution · 2025Article
- VILOCA: sequencing quality-aware viral haplotype reconstruction and mutation calling for short-read and long-read data.NAR genomics and bioinformatics · 2024Article
- V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation.GigaScience · 2024Article
Corrections and comments
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Authors and funding
19 authors.
Funding
Abstract
The large amount and diversity of viral genomic datasets generated by next-generation sequencing technologies poses a set of challenges for computational data analysis workflows, including rigorous quality control, scaling to large sample sizes, and tailored steps for specific applications. Here, we present V-pipe 3.0, a computational pipeline designed for analyzing next-generation sequencing data of short viral genomes. It is developed to enable reproducible, scalable, adaptable, and transparent inference of genetic diversity of viral samples. By presenting 2 large-scale data analysis projects, we demonstrate the effectiveness of V-pipe 3.0 in supporting sustainable viral genomic data science.
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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.