ArticleNature communications2022
Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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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
22 citing papers in PubMed.
- Anti-CRISPR-mediated continuous directed evolution of CRISPR-Cas9 in human cells.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- nTChap: an accurate method for polyploid haplotype reconstruction.BMC genomics · 2026Article
- Article
- Anti-CRISPR-mediated continuous directed evolution of CRISPR-Cas9 in human cells.bioRxiv : the preprint server for biology · 2025Article
- MicroRNAs in long COVID: roles, diagnostic biomarker potential and detection.Human genomics · 2025Review
- Characteristics and filtering of low-frequency artificial short deletion variations based on nanopore sequencing.GigaScience · 2025Article
- Deciphering mixed infections by plant RNA virus and reconstructing complete genomes simultaneously present within-host.PloS one · 2025Article
- Nanopore sequencing in veterinary medicine: from concepts to clinical applications.Frontiers in cellular and infection microbiology · 2025Review
- Machine learning-enhanced immunopeptidomics applied to T-cell epitope discovery for COVID-19 vaccines.Nature communications · 2024Article
- Unveiling microbial diversity: harnessing long-read sequencing technology.Nature methods · 2024Review
- Early detection of emerging viral variants through analysis of community structure of coordinated substitution networks.Nature communications · 2024Article
- Utility of long-read sequencing for All of Us.Nature communications · 2024Article
- A hepatitis B virus (HBV) sequence variation graph improves alignment and sample-specific consensus sequence construction.PloS one · 2024Article
- Review
- Nanopore sequencing technology and its applications.MedComm · 2023Review
- A hepatitis B virus (HBV) sequence variation graph improves sequence alignment and sample-specific consensus sequence construction for genetic analysis of HBV.bioRxiv : the preprint server for biology · 2023Article
- A Computer Simulation of SARS-CoV-2 Mutation Spectra for Empirical Data Characterization and Analysis.Biomolecules · 2022Article
- Early detection and improved genomic surveillance of SARS-CoV-2 variants from deep sequencing data.iScience · 2022Article
- Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data.Nature communications · 2022Article
- From Deer-to-Deer: SARS-CoV-2 is efficiently transmitted and presents broad tissue tropism and replication sites in white-tailed deer.PLoS pathogens · 2022Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Infectious disease monitoring on Oxford Nanopore Technologies (ONT) platforms offers rapid turnaround times and low cost. Tracking low frequency intra-host variants provides important insights with respect to elucidating within-host viral population dynamics and transmission. However, given the higher error rate of ONT, accurate identification of intra-host variants with low allele frequencies remains an open challenge with no viable computational solutions available. In response to this need, we present Variabel, a novel approach and first method designed for rescuing low frequency intra-host variants from ONT data alone. We evaluate Variabel on both synthetic data (SARS-CoV-2) and patient derived datasets (Ebola virus, norovirus, SARS-CoV-2); our results show that Variabel can accurately identify low frequency variants below 0.5 allele frequency, outperforming existing state-of-the-art ONT variant callers for this task. Variabel is open-source and available for download at: www.gitlab.com/treangenlab/variabel .
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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.