ArticleNature biotechnology2021
Readfish enables targeted nanopore sequencing of gigabase-sized genomes.
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 213 papers, 1 of them a synthesis that pooled it.
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Who cites it
213 citing papers in PubMed, 1 synthesis or guideline pooled it, 419 citations in OpenAlex.
- Nanopore Sequencing for Mycobacterium tuberculosis: a Critical Review of the Literature, New Developments, and Future Opportunities.Journal of clinical microbiology · 2022Pooled it
- Nanopore Sequencing for Chikungunya Virus: Principles and Application.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Nanopore Sequencing for Chikungunya Virus: Principles and Application.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Review
- Resolving missing human polymorphic inversions and other complex variants from ultralong read data.Genome research · 2026Article
- Unified long-read panel for Parkinson's and repeat expansion disorders.NPJ Parkinson's disease · 2026Article
- Accurate characterization of CRISPR-Cas9 genome editing outcomes and mosaicism with near-perfect long reads.Genome medicine · 2026Article
- Nanopore Ultra-Long Sequencing for FSHD: From Molecular Diagnosis to Preimplantation Genetic Testing.Genes · 2026Review
- Nanopore metagenomic sequencing links clinically relevant resistance determinants to pathogens.Microbial genomics · 2026Article
- Optical mapping reveals a higher level of large-scale structural variants in a family with paternally transmitted myotonic dystrophy and independent Parkinson's disease.The Journal of pathology · 2026Article
- Toward the clinical application of long-read sequencing in repeat-expansion disorders.Nature genetics · 2026Review
- Haplotype-resolved DiMeLo-seq maps centromeric chromatin in a complete diploid human genome.Cell genomics · 2026Article
- Targeted long-read sequencing enables comprehensive analysis of the genetic and epigenetic landscape of inherited myopathies.Nature communications · 2026Article
- Long-read sequencing reveals SVA insertion in AP3B1 causing Hermansky-Pudlak syndrome 2.Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology · 2026Article
- Detection of heteroresistance in Mycobacterium tuberculosis using nanopore-based amplicon sequencing and adaptive sampling.Scientific reports · 2026Article
- Genome-guided generative adversarial learning enables nanopore adaptive sequencing.Nature communications · 2026Article
- From fragments to full pictures: how long-read sequencing platforms are revolutionizing oncology research.Molecular biology reports · 2026Review
- 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
- 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
153 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
Nanopore sequencers can be used to selectively sequence certain DNA molecules in a pool by reversing the voltage across individual nanopores to reject specific sequences, enabling enrichment and depletion to address biological questions. Previously, we achieved this using dynamic time warping to map the signal to a reference genome, but the method required substantial computational resources and did not scale to gigabase-sized references. Here we overcome this limitation by using graphical processing unit (GPU) base-calling. We show enrichment of specific chromosomes from the human genome and of low-abundance organisms in mixed populations without a priori knowledge of sample composition. Finally, we enrich targeted panels comprising 25,600 exons from 10,000 human genes and 717 genes implicated in cancer, identifying PML-RARA fusions in the NB4 cell line in <15 h sequencing. These methods can be used to efficiently screen any target panel of genes without specialized sample preparation using any computer and a suitable GPU. Our toolkit, readfish, is available at https://www.github.com/looselab/readfish .
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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.