ArticleGigaScience2018
NanoAmpli-Seq: a workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform.
Article in GigaScience, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
48 citing papers in PubMed.
- Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota.PloS one · 2021Trial
- CLAE: A High-Fidelity Nanopore Sequencing Strategy for Read-Level Viral Variant Detection and Environmental RNA Virus Discovery.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- A species-level identification pipeline for human gut microbiota based on the V3-V4 regions of 16S rRNA.Frontiers in microbiology · 2025Article
- Coral garden conservation and restoration: how host taxon andFrontiers in microbiology · 2025Article
- Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data.Briefings in bioinformatics · 2024Article
- High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the Nanopore platform.PNAS nexus · 2024Article
- Primed and ready: nanopore metabarcoding can now recover highly accurate consensus barcodes that are generally indel-free.BMC genomics · 2024Article
- Article
- Exploiting long read sequencing to detect azole fungicide resistance mutations in Pyrenophora teres using unique molecular identifiers.Scientific reports · 2024Article
- An integrative protocol for one-step PCR amplicon library construction and accurate demultiplexing of pooled sequencing data.Marine life science & technology · 2023Article
- Single-worm long-read sequencing reveals genome diversity in free-living nematodes.Nucleic acids research · 2023Article
- Analysis of Lung Microbiome in COVID-19 Patients during Time of Hospitalization.Pathogens (Basel, Switzerland) · 2023Article
- Article
- Species-Level Characterization of the Microbiome in Breast Tissues with Different Malignancy and Hormone-Receptor Statuses Using Nanopore Sequencing.Journal of personalized medicine · 2023Article
- High-resolution phylogenetic and population genetic analysis of microbial communities with RoC-ITS.ISME communications · 2022Article
- Article
- Clinical Performance of Nanopore Targeted Sequencing for Diagnosing Infectious Diseases.Microbiology spectrum · 2022Article
- Amplicon_sorter: A tool for reference-free amplicon sorting based on sequence similarity and for building consensus sequences.Ecology and evolution · 2022Article
- Long-Amplicon Single-Molecule Sequencing Reveals Novel, Trait-Associated Variants ofFrontiers in plant science · 2022Article
- Nanopore sequencing technology, bioinformatics and applications.Nature biotechnology · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Background: Amplicon sequencing on Illumina sequencing platforms leverages their deep sequencing and multiplexing capacity but is limited in genetic resolution due to short read lengths. While Oxford Nanopore or Pacific Biosciences sequencing platforms overcome this limitation, their application has been limited due to higher error rates or lower data output. Results: In this study, we introduce an amplicon sequencing workflow, i.e., NanoAmpli-Seq, that builds on the intramolecular-ligated nanopore consensus sequencing (INC-Seq) approach and demonstrate its application for full-length 16S rRNA gene sequencing. NanoAmpli-Seq includes vital improvements to the INC-Seq protocol that reduces sample processing time while significantly improving sequence accuracy. The developed protocol includes chopSeq software for fragmentation and read orientation correction of INC-Seq consensus reads while nanoClust algorithm was designed for read partitioning-based de novo clustering and within cluster consensus calling to obtain accurate full-length 16S rRNA gene sequences. Conclusions: NanoAmpli-Seq accurately estimates the diversity of tested mock communities with average consensus sequence accuracy of 99.5% for 2D and 1D2 sequencing on the nanopore sequencing platform. Nearly all residual errors in NanoAmpli-Seq sequences originate from deletions in homopolymer regions, indicating that homopolymer aware base calling or error correction may allow for sequencing accuracy comparable to short-read sequencing platforms.
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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.