ArticleFrontiers in microbiology2022
Systematic benchmarking of nanopore Q20+ kit in SARS-CoV-2 whole genome sequencing.
Article in Frontiers in microbiology, 2022. 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 29 papers.
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Who cites it
29 citing papers in PubMed, 43 citations in OpenAlex.
- SARS-CoV-2 wastewater genomic surveillance: approaches, challenges, and opportunities.Genome biology · 2026Review
- EZ-DMS - A Simple and Accessible Protocol and Software Package for Deep Mutational Scanning of Virus Proteins.bioRxiv : the preprint server for biology · 2026Article
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- CCS-Consensuser: A Haplotype-Aware Consensus Generator for PacBio Amplicon Sequences.Molecular ecology resources · 2025Article
- Accurate and Cost-Efficient Whole Genome Sequencing of Hepatitis B Virus Using Nanopore.Journal of medical virology · 2025Article
- Article
- Enhancing public health surveillance: a comparative study of platform-specific and hybrid assembly approaches in SARS-CoV-2 genome sequencing.Microbial genomics · 2025Article
- Impact of microbiological molecular methodologies on adaptive sampling using nanopore sequencing in metagenomic studies.Environmental microbiome · 2025Article
- GoldPolish-target: targeted long-read genome assembly polishing.BMC bioinformatics · 2025Article
- Long-Read Sequencing for the Rapid Response to Infectious Diseases Outbreaks.Current clinical microbiology reports · 2025Review
- Prevalences of respiratory viruses and bacteria in Western Canadian commercial feedlot calves detected using a single metagenomic sequencing protocol vary during the first two weeks of arrival and by age group.Frontiers in veterinary science · 2025Article
- Global trends in the application of nanopore sequencing technology in the detection of infectious disease pathogens: a bibliometric analysis from 2014 to 2024.Frontiers in medicine · 2025Article
- Nanopore Data-Driven T2T Genome Assemblies ofJournal of fungi (Basel, Switzerland) · 2024Article
- Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data.Briefings in bioinformatics · 2024Article
- Amplified DNA Heterogeneity Assessment with Oxford Nanopore Sequencing Applied to Cell Free Expression Templates.bioRxiv : the preprint server for biology · 2024Article
- Isoform-specific RNA structure determination using Nano-DMS-MaP.Nature protocols · 2024Review
- An evolution of Nanopore next-generation sequencing technology: implications for medical microbiology and public health.Journal of clinical microbiology · 2024Article
- Meat-Borne-Parasite: A Nanopore-Based Meta-Barcoding Work-Flow for Parasitic Microbiodiversity Assessment in the Wild Fauna of French Guiana.Current issues in molecular biology · 2024Article
- Article
- Amplified DNA heterogeneity assessment with Oxford Nanopore sequencing applied to cell free expression templates.PloS one · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
10 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole genome sequencing provides rapid insight into key information about the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), such as virus typing and key mutation site, and this information is important for precise prevention, control and tracing of coronavirus disease 2019 (COVID-19) outbreak in conjunction with the epidemiological information of the case. Nanopore sequencing is widely used around the world for its short sample-to-result time, simple experimental operation and long sequencing reads. However, because nanopore sequencing is a relatively new sequencing technology, many researchers still have doubts about its accuracy. The combination of the newly launched nanopore sequencing Q20+ kit (LSK112) and flow cell R10.4 is a qualitative improvement over the accuracy of the previous kits. In this study, we firstly used LSK112 kit with flow cell R10.4 to sequence the SARS-CoV-2 whole genome, and summarized the sequencing results of the combination of LSK112 kit and flow cell R10.4 for the 1200bp amplicons of SARS-CoV-2. We found that the proportion of sequences with an accuracy of more than 99% reached 30.1%, and the average sequence accuracy reached 98.34%, while the results of the original combination of LSK109 kit and flow cell R9.4.1 were 0.61% and 96.52%, respectively. The mutation site analysis showed that it was completely consistent with the final consensus sequence of next generation sequencing (NGS). The results showed that the combination of LSK112 kit and flow cell R10.4 allowed rapid whole-genome sequencing of SARS-CoV-2 without the need for verification of NGS.
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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.