ArticleNature methods2021
High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing.
Article in Nature methods, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 226 papers, 2 of them syntheses that pooled it.
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Who cites it
226 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Systematic Review: Long-Read Sequencing in Algal Studies.International journal of molecular sciences · 2026Pooled it
- The Relationship Between the Gut Microbiome and the Aqua Cultured Fish, General Prospects Toward Fish Health: A Systematic Review.Applied biochemistry and biotechnology · 2025Pooled it
- Early-life microbiota in the LIMIT cohort: unveiling meconium microbiota types beyond maternal lifestyle.Gut microbes · 2026Article
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- A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq nanopore long reads data.NAR genomics and bioinformatics · 2026Article
- Analysing long-read CRISPR experiments with CRISPRLungo.Nature biomedical engineering · 2026Article
- Analysis of Rhizosphere Microbial Diversity Among Different Maize Varieties in the Hexi Corridor.Microorganisms · 2026Article
- Benchmarking Full-Length ITS Metabarcoding Across Illumina 2 × 500, PacBio, and Oxford Nanopore Sequencing Using Mock and Soil Communities.Molecular ecology resources · 2026Article
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- BASELINE: a CRISPR base editing platform for mammalian-scale single-cell lineage tracing.Nucleic acids research · 2026Article
- An SLCO2B1 mRNA Isoform Acts as a Noncoding RNA to Drive Cancer Progression by Triggering Protein Biosynthesis.Cancer research · 2026Article
- Barbell reveals and resolves demultiplexing and trimming issues in Nanopore data.Bioinformatics (Oxford, England) · 2026Article
- Biosensing With Nanofluidics.Exploration (Beijing, China) · 2026Review
- A high-quality bread wheat genome unravels the adaptive evolution of wheat end-use quality.Nature plants · 2026Article
- A Scalable and Cost-Effective In-Line Barcoding Strategy for Standardized 16S rRNA Gene Amplicon Sequencing: Performance Evaluation and Bias Assessment.Molecular ecology resources · 2026Article
- Prenatal Whole-Genome Sequencing for Fetal Anomalies: Diagnostic Performance, Challenges, and Clinical Implications.International journal of molecular sciences · 2026Review
- Oxford Nanopore enhanced accuracy of long-read amplicons applied to microbial whole-genome sequencing.Microbiology spectrum · 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
- 6 mA methylation differences in Riccia fluitans organellar genomes under flood stress.Plant cell reports · 2026Article
166 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput amplicon sequencing of large genomic regions remains challenging for short-read technologies. Here, we report a high-throughput amplicon sequencing approach combining unique molecular identifiers (UMIs) with Oxford Nanopore Technologies (ONT) or Pacific Biosciences circular consensus sequencing, yielding high-accuracy single-molecule consensus sequences of large genomic regions. We applied our approach to sequence ribosomal RNA operon amplicons (~4,500 bp) and genomic sequences (>10,000 bp) of reference microbial communities in which we observed a chimera rate <0.02%. To reach a mean UMI consensus error rate <0.01%, a UMI read coverage of 15× (ONT R10.3), 25× (ONT R9.4.1) and 3× (Pacific Biosciences circular consensus sequencing) is needed, which provides a mean error rate of 0.0042%, 0.0041% and 0.0007%, respectively.
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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.