ArticleNucleic acids research2019
Direct sequencing of RNA with MinION Nanopore: detecting mutations based on associations.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed.
- DnaJ mediates phage sensing by the bacterial NLR-related protein bNACHT25.PLoS biology · 2025Article
- Transcriptome-wide identification of 5-methylcytosine by deaminase and reader protein-assisted sequencing.eLife · 2025Article
- Deciphering mixed infections by plant RNA virus and reconstructing complete genomes simultaneously present within-host.PloS one · 2025Article
- Analytical Performance of a Novel Nanopore Sequencing for SARS-CoV-2 Genomic Surveillance.Journal of medical virology · 2024Article
- Analysis of Coinfection Pathogens From Foot-and-Mouth Disease Virus Persistently Infected Cattle Using Oxford Nanopore Sequencing.Transboundary and emerging diseases · 2024Article
- Shared sequence characteristics identified in non-canonical rearrangements of HSV-1 genomes.Journal of virology · 2023Article
- Genomic characterization of SARS-CoV-2 from Uganda using MinION nanopore sequencing.Scientific reports · 2023Article
- Article
- AccuVIR: an ACCUrate VIRal genome assembly tool for third-generation sequencing data.Bioinformatics (Oxford, England) · 2023Article
- Extent and complexity of RNA processing in honey bee queen and worker caste development.iScience · 2022Article
- Tracing the SARS-CoV-2 infection on the ocular surface: Overview and preliminary corneoscleral transcriptome sequencing.Experimental eye research · 2022Article
- VirStrain: a strain identification tool for RNA viruses.Genome biology · 2022Article
- Grapevine Virology in the Third-Generation Sequencing Era: From Virus Detection to Viral Epitranscriptomics.Plants (Basel, Switzerland) · 2021Review
- Rapid Acquisition of High-Quality SARS-CoV-2 Genome via Amplicon-Oxford Nanopore Sequencing.Virologica Sinica · 2021Article
- Article
- Is Oxford Nanopore sequencing ready for analyzing complex microbiomes?FEMS microbiology ecology · 2021Article
- Direct oligonucleotide sequencing with nanopores.Open research Europe · 2021Article
- Genetic Identification and Drug-Resistance Characterization ofAntibiotics (Basel, Switzerland) · 2020Article
- Competition between social cheater viruses is driven by mechanistically different cheating strategies.Science advances · 2020Article
- Determining the Suitability of MinION's Direct RNA and DNA Amplicon Sequencing for Viral Subtype Identification.Viruses · 2020Article
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
One of the key challenges in the field of genetics is the inference of haplotypes from next generation sequencing data. The MinION Oxford Nanopore sequencer allows sequencing long reads, with the potential of sequencing complete genes, and even complete genomes of viruses, in individual reads. However, MinION suffers from high error rates, rendering the detection of true variants difficult. Here, we propose a new statistical approach named AssociVar, which differentiates between true mutations and sequencing errors from direct RNA/DNA sequencing using MinION. Our strategy relies on the assumption that sequencing errors will be dispersed randomly along sequencing reads, and hence will not be associated with each other, whereas real mutations will display a non-random pattern of association with other mutations. We demonstrate our approach using direct RNA sequencing data from evolved populations of the MS2 bacteriophage, whose small genome makes it ideal for MinION sequencing. AssociVar inferred several mutations in the phage genome, which were corroborated using parallel Illumina sequencing. This allowed us to reconstruct full genome viral haplotypes constituting different strains that were present in the sample. Our approach is applicable to long read sequencing data from any organism for accurate detection of bona fide mutations and inter-strain polymorphisms.
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.