ArticleScientific reports2019
Real-Time Selective Sequencing with RUBRIC: Read Until with Basecall and Reference-Informed Criteria.
Article in Scientific reports, 2019. 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 45 papers.
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Who cites it
45 citing papers in PubMed.
- 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
- Assessment of the effectiveness of host depletion techniques for profiling fish skin microbiomes and metagenomic analysis.Microbiology spectrum · 2026Article
- A comprehensive benchmarking of adaptive sampling tools for nanopore sequencing.Genome biology · 2025Article
- Targeted sequencing ofmSystems · 2025Article
- Nanopore adaptive sampling to identify the NLR gene family in melon (Cucumis melo L.).BMC genomics · 2025Article
- Navigating triplet repeats sequencing: concepts, methodological challenges and perspective for Huntington's disease.Nucleic acids research · 2025Review
- Environmental epigenomics and the human imprintome.Environmental epigenetics · 2025Article
- Rapid Detection ofBiomolecules · 2024Article
- Real-time and programmable transcriptome sequencing with PROFIT-seq.Nature cell biology · 2024Article
- Leveraging the power of long reads for targeted sequencing.Genome research · 2024Review
- Advances in Host Depletion and Pathogen Enrichment Methods for Rapid Sequencing-Based Diagnosis of Bloodstream Infection.The Journal of molecular diagnostics : JMD · 2024Review
- ReadCurrent: a VDCNN-based tool for fast and accurate nanopore selective sequencing.Briefings in bioinformatics · 2024Article
- Direct RNA sequencing coupled with adaptive sampling enriches RNAs of interest in the transcriptome.Nature communications · 2024Article
- Genome-resolved metatranscriptomics reveals conserved root colonization determinants in a synthetic microbiota.Nature communications · 2023Article
- Adaptive sampling for nanopore direct RNA-sequencing.RNA (New York, N.Y.) · 2023Article
- NanoDeep: a deep learning framework for nanopore adaptive sampling on microbial sequencing.Briefings in bioinformatics · 2023Article
- Beyond assembly: the increasing flexibility of single-molecule sequencing technology.Nature reviews. Genetics · 2023Review
- RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes.Bioinformatics (Oxford, England) · 2023Article
- Best Practices in Microbial Experimental Evolution: Using Reporters and Long-Read Sequencing to Identify Copy Number Variation in Experimental Evolution.Journal of molecular evolution · 2023Review
Corrections and comments
- Erratum issued
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Oxford MinION, the first commercial nanopore sequencer, is also the first to implement molecule-by-molecule real-time selective sequencing or "Read Until". As DNA transits a MinION nanopore, real-time pore current data can be accessed and analyzed to provide active feedback to that pore. Fragments of interest are sequenced by default, while DNA deemed non-informative is rejected by reversing the pore bias to eject the strand, providing a novel means of background depletion and/or target enrichment. In contrast to the previously published pattern-matching Read Until approach, our RUBRIC method is the first example of real-time selective sequencing where on-line basecalling enables alignment against conventional nucleic acid references to provide the basis for sequence/reject decisions. We evaluate RUBRIC performance across a range of optimizable parameters, apply it to mixed human/bacteria and CRISPR/Cas9-cut samples, and present a generalized model for estimating real-time selection performance as a function of sample composition and computing configuration.
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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.