ArticleNature biotechnology2021
Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED.
Article in Nature biotechnology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 158 papers.
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Who cites it
158 citing papers in PubMed, 276 citations in OpenAlex.
- Review
- Resolving missing human polymorphic inversions and other complex variants from ultralong read data.Genome research · 2026Article
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- Nanopore Ultra-Long Sequencing for FSHD: From Molecular Diagnosis to Preimplantation Genetic Testing.Genes · 2026Review
- Toward the clinical application of long-read sequencing in repeat-expansion disorders.Nature genetics · 2026Review
- Human wastewater contamination drives the emergence of multidrug-resistant bacteria in the Galápagos marine ecosystem.Nature communications · 2026Article
- Movi 2: fast and space-efficient queries on pangenomes.Bioinformatics (Oxford, England) · 2026Article
- The mRNA covalent modification dihydrouridine regulates transcript turnover and photosynthetic capacity during plant abiotic stress.The Plant cell · 2026Article
- Feasibility of long-read nanopore sequencing for methylation-based classification of posterior fossa ependymomas.Brain tumor pathology · 2026Article
- Genome-guided generative adversarial learning enables nanopore adaptive sequencing.Nature communications · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Flexible and rapid validation of structural variation using adaptive sampling.European journal of human genetics : EJHG · 2026Article
- From spacecraft ranging to massive DNA data storage: Composite ranging codes as indices and error correction references.Science advances · 2026Article
- Umi-pipeline-nf: a modular and scalable workflow for UMI-tagged nanopore amplicon analysis with real-time sequencing integration and GPU-acceleration.Bioinformatics (Oxford, England) · 2026Article
- Article
- MASTR-seq enables multiplexed analysis of short tandem repeats with sequencing.Cell reports methods · 2026Article
- SquiDBase: a community resource of raw nanopore data from microbes.NAR genomics and bioinformatics · 2026Article
- Advancing Plant Microbiome Research Through Host DNA Depletion Techniques.Plant biotechnology journal · 2026Review
- Rawsamble: overlapping raw nanopore signals using a hash-based seeding mechanism.Bioinformatics (Oxford, England) · 2026Article
- Campolina: a deep neural framework for accurate segmentation of nanopore signals.Genome biology · 2026Article
98 more citing papers are in PubMed but not listed here.
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5 authors at 1 institution in 1 country.
Funding
Abstract
Conventional targeted sequencing methods eliminate many of the benefits of nanopore sequencing, such as the ability to accurately detect structural variants or epigenetic modifications. The ReadUntil method allows nanopore devices to selectively eject reads from pores in real time, which could enable purely computational targeted sequencing. However, this requires rapid identification of on-target reads while most mapping methods require computationally intensive basecalling. We present UNCALLED ( https://github.com/skovaka/UNCALLED ), an open source mapper that rapidly matches streaming of nanopore current signals to a reference sequence. UNCALLED probabilistically considers k-mers that could be represented by the signal and then prunes the candidates based on the reference encoded within a Ferragina-Manzini index. We used UNCALLED to deplete sequencing of known bacterial genomes within a metagenomics community, enriching the remaining species 4.46-fold. UNCALLED also enriched 148 human genes associated with hereditary cancers to 29.6× coverage using one MinION flowcell, enabling accurate detection of single-nucleotide polymorphisms, insertions and deletions, structural variants and methylation in these genes.
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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.