ArticleNature methods2015
Improved data analysis for the MinION nanopore sequencer.
Article in Nature methods, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 292 papers.
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Who cites it
292 citing papers in PubMed, 686 citations in OpenAlex.
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- Long-read sequencing technologies and bioinformatics: a new perspective for decoding DNA methylation modifications.Journal of translational medicine · 2026Review
- Nanopore direct RNA sequencing (DRS) of MS2 bacteriophages in E. coli throughout its life cycles reveals a complex transcriptional activity to control and maintain its growth.Virology journal · 2026Article
- Bioinformatic and computational biophysics tools for nanopore engineering: a review from standard approaches to machine learning advancements.Journal of nanobiotechnology · 2026Review
- High-Resolution Community Profiling of Active Bacteria and Eukaryotes in Replant-Diseased Blueberry Farm Soils From New Jersey, USA.Environmental microbiology · 2026Article
- LncRNAs in Ovarian Cancer: Emerging Insights and Future Perspectives in Tumor Biology and Clinical Applications.Cancers · 2026Review
- NanoporeDB: a structural resource of multimeric protein nanopores for single-molecule sensing.GigaScience · 2026Article
- Detecting foldback artifacts in long-reads.BMC genomics · 2026Article
- Genetic diversity and architectural dynamics of soybean centromeres.Genome biology · 2026Article
- Detecting Foldback Artifacts in Long-reads.bioRxiv : the preprint server for biology · 2025Article
- The applications and advantages of nanopore sequencing in bacterial antimicrobial resistance surveillance and research.npj antimicrobials and resistance · 2025Review
- The Role of Nucleotide Sequencing in Natural Product Drug Discovery.Journal of natural products · 2025Review
- An ancient regulatory variant of ACSF3 influences the coevolution of increased human height and basal metabolic rate via metabolic homeostasis.Cell genomics · 2025Article
- Overview of Microorganisms: Bacterial Microbiome, Mycobiome, Virome Identified Using Next-Generation Sequencing, and Their Application to Ophthalmic Diseases.Microorganisms · 2025Review
- The Long and the Short of It: Nanopore-Based eDNA Metabarcoding of Marine Vertebrates Works; Sensitivity and Species-Level Assignment Depend on Amplicon Lengths.Molecular ecology resources · 2025Article
- Barcode-free multiplex plasmid sequencing using Bayesian analysis and nanopore sequencing.eLife · 2025Article
- Nanopore sequencing for precise detection ofJournal of clinical microbiology · 2025Article
- Study on the early diagnostic value of nanopore sequencing in alveolar lavage fluid smear-negative pulmonary tuberculosis.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2025Article
232 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Speed, single-base sensitivity and long read lengths make nanopores a promising technology for high-throughput sequencing. We evaluated and optimized the performance of the MinION nanopore sequencer using M13 genomic DNA and used expectation maximization to obtain robust maximum-likelihood estimates for insertion, deletion and substitution error rates (4.9%, 7.8% and 5.1%, respectively). Over 99% of high-quality 2D MinION reads mapped to the reference at a mean identity of 85%. We present a single-nucleotide-variant detection tool that uses maximum-likelihood parameter estimates and marginalization over many possible read alignments to achieve precision and recall of up to 99%. By pairing our high-confidence alignment strategy with long MinION reads, we resolved the copy number for a cancer-testis gene family (CT47) within an unresolved region of human chromosome Xq24.
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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.