ArticleNature communications2021
Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 92 papers.
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Who cites it
92 citing papers in PubMed.
- Long-read sequencing for neurological disorders: opportunities, challenges, and future directions.Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology · 2026Review
- SpliSync: Genomic language model-driven splice site correction of long RNA sequencing reads.bioRxiv : the preprint server for biology · 2026Article
- Fungen: clustering and correcting long-read metatranscriptomic data for exploring eukaryotic microorganisms.Science China. Life sciences · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- QoALa: A comprehensive workflow for viral quasispecies diversity comparison using long-read sequencing data.PLoS computational biology · 2026Article
- Genomic insights intoMicrobiology spectrum · 2026Article
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- NanoPrePro: a fully equipped, fast, and memory-efficient preprocessor for nanopore transcriptomic sequencing.Briefings in bioinformatics · 2026Article
- Full-length transcriptome ofPlant biotechnology (Tokyo, Japan) · 2025Article
- DemuxTrans: Transformer and temporal convolution network for accurate barcode demultiplexing in nanopore sequencing.Bioinformatics (Oxford, England) · 2025Article
- Shaping Precision Medicine: The Journey of Sequencing Technologies Across Human Solid Tumors.Biomedicines · 2025Review
- Combining panel-based and whole-transcriptome-based gene fusion detection by long-read sequencing.Cell reports methods · 2025Article
- Transduction of Lentiviral Vectors andInternational journal of molecular sciences · 2025Article
- De novo clustering of large long-read transcriptome datasets with isONclust3.Bioinformatics (Oxford, England) · 2025Article
- Advanced analysis of retrotransposon variation in the human genome with nanopore sequencing using RetroInspector.Scientific reports · 2025Article
- Barcode-free multiplex plasmid sequencing using Bayesian analysis and nanopore sequencing.eLife · 2025Article
- Pragmatic soft-decision data readout of encoded large DNA.Briefings in bioinformatics · 2025Article
- Article
- A Complete Assembly and Annotation of the American Shad Genome Yields Insights into the Origins of Diadromy.Genome biology and evolution · 2025Article
- cONcat: Computational reconstruction of concatenated fragments from long Oxford Nanopore reads.PloS one · 2025Article
32 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
2 authors.
Funding
Abstract
Oxford Nanopore (ONT) is a leading long-read technology which has been revolutionizing transcriptome analysis through its capacity to sequence the majority of transcripts from end-to-end. This has greatly increased our ability to study the diversity of transcription mechanisms such as transcription initiation, termination, and alternative splicing. However, ONT still suffers from high error rates which have thus far limited its scope to reference-based analyses. When a reference is not available or is not a viable option due to reference-bias, error correction is a crucial step towards the reconstruction of the sequenced transcripts and downstream sequence analysis of transcripts. In this paper, we present a novel computational method to error correct ONT cDNA sequencing data, called isONcorrect. IsONcorrect is able to jointly use all isoforms from a gene during error correction, thereby allowing it to correct reads at low sequencing depths. We are able to obtain a median accuracy of 98.9-99.6%, demonstrating the feasibility of applying cost-effective cDNA full transcript length sequencing for reference-free transcriptome analysis.
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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.