ArticleScientific reports2019
Assessment of low-coverage nanopore long read sequencing for SNP genotyping in doubled haploid canola (Brassica napus L.).
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
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- Genomic structural variation rescues a classic biological invader from a population bottleneck.Science advances · 2026Article
- Benchmarking of real-time, field-deployable whole-genome sequencing ofMicrobial genomics · 2026Article
- Enhancing whole genome DNA amplification of Plasmodium falciparum for advanced molecular surveillance in malaria control.Malaria journal · 2025Article
- A low-coverage skim-sequencing and imputation pipeline for genomic selection.The plant genome · 2025Article
- Forensic DNA phenotyping using Oxford Nanopore Sequencing system.Electrophoresis · 2025Article
- Long-Range Targeted Nanopore Ligation Sequencing Workflow for Targeted Amplicon Sequencing of Secondary Metabolite Gene.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Whole-genome comparison using complete genomes fromFrontiers in microbiology · 2024Article
- Evaluating the potential of (epi)genotype-by-low pass nanopore sequencing in dairy cattle: a study on direct genomic value and methylation analysis.Journal of animal science and biotechnology · 2023Article
- Application of Nanopore Sequencing for High Throughput Genotyping in Horses.Animals : an open access journal from MDPI · 2023Article
- Shoot-root signal circuit: Phytoremediation of heavy metal contaminated soil.Frontiers in plant science · 2023Review
- Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph.BMC bioinformatics · 2021Article
- Long-Read Sequencing Improves the Detection of Structural Variations Impacting Complex Non-Coding Elements of the Genome.International journal of molecular sciences · 2021Article
- The Future of Livestock Management: A Review of Real-Time Portable Sequencing Applied to Livestock.Genes · 2020Review
- Oxford Nanopore sequencing: new opportunities for plant genomics?Journal of experimental botany · 2020Article
- Rapid and Detailed Characterization of Transgene Insertion Sites in Genetically Modified Plants via Nanopore Sequencing.Frontiers in plant science · 2020Article
- Long-read genotyping with SLANG (Simple Long-read loci Assembly of Nanopore data for Genotyping).Applications in plant sciencesArticle
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite the high accuracy of short read sequencing (SRS), there are still issues with attaining accurate single nucleotide polymorphism (SNP) genotypes at low sequencing coverage and in highly duplicated genomes due to misalignment. Long read sequencing (LRS) systems, including the Oxford Nanopore Technologies (ONT) minION, have become popular options for de novo genome assembly and structural variant characterisation. The current high error rate often requires substantial post-sequencing correction and would appear to prevent the adoption of this system for SNP genotyping, but nanopore sequencing errors are largely random. Using low coverage ONT minION sequencing for genotyping of pre-validated SNP loci was examined in 9 canola doubled haploids. The minION genotypes were compared to the Illumina sequences to determine the extent and nature of genotype discrepancies between the two systems. The significant increase in read length improved alignment to the genome and the absence of classical SRS biases results in a more even representation of the genome. Sequencing errors are present, primarily in the form of heterozygous genotypes, which can be removed in completely homozygous backgrounds but requires more advanced bioinformatics in heterozygous genomes. Developments in this technology are promising for routine genotyping in the future.
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