ArticleGenome research2019
Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome.
Article in Genome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers.
What it found
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Who cites it
101 citing papers in PubMed.
- Uncovering structural variation in conifer gigagenomes: evolutionary insights and technical challenges.Molecular biology and evolution · 2026Article
- European ash pangenome reveals widespread structural variation and genetic basis of low ash dieback susceptibility.Nature communications · 2026Article
- Resolving CYP2D6 Structural Complexity with Long-Read Sequencing: Implications for Tamoxifen Precision Dosing in Thai Breast Cancer Patients.Clinical pharmacology and therapeutics · 2026Article
- Long-Read Sequencing in CKD Diagnostics: Breaking Genomic Barriers and Expanding Global Inclusion.Kidney international reports · 2026Review
- Complementarity of Long-Reads and Optical Mapping in Parkinson's Disease for Structural Variants.Annals of clinical and translational neurology · 2026Article
- NanoSimFormer: an end-to-end transformer-based nanopore signal simulator with basecaller guidance.Bioinformatics (Oxford, England) · 2026Article
- Genetic demultiplexing and transcript start site identification from nanopore sequencing of 10x Genomics multiome libraries.bioRxiv : the preprint server for biology · 2026Article
- NanoVar: a comprehensive workflow for structural variant detection to uncover the genome's hidden patterns.Nature protocols · 2026Review
- Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications.Genome research · 2026Article
- An allele-resolved nanopore-guided tour of the human placental methylome.Nature communications · 2025Article
- NANOME: A Nextflow pipeline for haplotype-aware allele-specific consensus DNA methylation detection by nanopore long-read sequencing.bioRxiv : the preprint server for biology · 2025Article
- A 69.9-kb long inverted repeat increases genome instability in a strain ofNAR genomics and bioinformatics · 2025Article
- Parental Phasing Study Identified Lineage-Specific Variants Associated with Gene Expression and Epigenetic Modifications in European-Chinese Hybrid Pigs.Animals : an open access journal from MDPI · 2025Article
- Advanced analysis of retrotransposon variation in the human genome with nanopore sequencing using RetroInspector.Scientific reports · 2025Article
- The known structural variations in hearing loss and their diagnostic approaches: a comprehensive review.Molecular biology reports · 2025Review
- Toward a standardized framework for pangenome graph evaluation: assessing crop plant pangenome variation graph construction from multiple assemblies.GigaScience · 2025Article
- AI-powered analysis of viral metagenomic sequencing data for rapid outbreak investigation and novel pathogen discovery.Frontiers in microbiology · 2025Review
- Genome-wide characterization of structure variations in the Xiang pig for genetic resistance to African swine fever.Virulence · 2024Article
- Benchmarking long-read aligners and SV callers for structural variation detection in Oxford nanopore sequencing data.Scientific reports · 2024Article
- A chromosome-level genome assembly of a free-living white-crowned sparrow (Zonotrichia leucophrys gambelii).Scientific data · 2024Article
41 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
We sequenced the genome of the Yoruban reference individual NA19240 on the long-read sequencing platform Oxford Nanopore PromethION for evaluation and benchmarking of recently published aligners and germline structural variant calling tools, as well as a comparison with the performance of structural variant calling from short-read sequencing data. The structural variant caller Sniffles after NGMLR or minimap2 alignment provides the most accurate results, but additional confidence or sensitivity can be obtained by a combination of multiple variant callers. Sensitive and fast results can be obtained by minimap2 for alignment and a combination of Sniffles and SVIM for variant identification. We describe a scalable workflow for identification, annotation, and characterization of tens of thousands of structural variants from long-read genome sequencing of an individual or population. By discussing the results of this well-characterized reference individual, we provide an approximation of what can be expected in future long-read sequencing studies aiming for structural variant identification.
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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.