ArticleInternational journal of molecular sciences2025
Investigating the Performance of Oxford Nanopore Long-Read Sequencing with Respect to Illumina Microarrays and Short-Read Sequencing.
Article in International journal of molecular sciences, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.
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Who cites it
17 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Long-Read sequencing in psychiatric omics: a systematic review of current evidence.Molecular psychiatry · 2026Pooled it
- Unified long-read panel for Parkinson's and repeat expansion disorders.NPJ Parkinson's disease · 2026Article
- Bacterial metagenomic analysis of patients with chronic kidney disease undergoing hemodialysis based on 16S rDNA amplicon sequencing.Biomedical reports · 2026Article
- Near-real-time whole-genome sequencing in hospital infection control: a narrative review.Infection · 2026Review
- The Genetic Landscape of Fibrotic Interstitial Lung Diseases: Clinical Implications and Diagnostic Challenges in Familial Pulmonary Fibrosis.Journal of clinical medicine · 2026Review
- From variants to answers: The evolution of genetic counseling in IEI.Journal of human immunity · 2026Review
- Benchmarking of sequencing technologies defines optimal strategies for genetic variants detection in a human genome.Genome biology · 2026Article
- Long-read Sequencing in Inherited Retinal Dystrophies: A Systematic Review.Ophthalmology science · 2026Review
- Comparative Analysis of Next- and Third-Generation Sequencing Platforms for Chikungunya Virus Whole-Genome Sequencing Using a Lineage-Inclusive Primer Set During the 2025 Foshan Outbreak.Tropical medicine and infectious disease · 2026Article
- Comparative Evaluation of Sequencing Technologies for Detecting Antimicrobial Resistance in Bloodstream Infections.Antibiotics (Basel, Switzerland) · 2025Review
- Long-range PCR and Nanopore sequencing for localisation and phasing variants: an end-to-end clinical application workflow.BMC medical genomics · 2025Article
- CCS-Consensuser: A Haplotype-Aware Consensus Generator for PacBio Amplicon Sequences.Molecular ecology resources · 2025Article
- Methodological Comparison of Short-Read and Long-Read Sequencing Methods on Colorectal Cancer Samples.International journal of molecular sciences · 2025Article
- Variation of and associations with the depth and evenness of sequencing coverage in archived plastid genomes.Scientific reports · 2025Article
- Variation of and associations with the depth and evenness of sequencing coverage in archived plastid genomes.Research square · 2025Article
- Modelling Population Genetic Screening in Rare Neurodegenerative Diseases.Biomedicines · 2025Article
- Nanopore targeted sequencing in lower respiratory infections: a retrospective study on diagnostic applications, clinical characterization, and antimicrobial guidance.Frontiers in cellular and infection microbiology · 2025Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Oxford Nanopore Technologies (ONT) long-read sequencing (LRS) has emerged as a promising genomic analysis tool, yet comprehensive benchmarks with established platforms across diverse datasets remain limited. This study aimed to benchmark LRS performance against Illumina short-read sequencing (SRS) and microarrays for variant detection across different genomic contexts and to evaluate the impact of experimental factors. We sequenced 14 human genomes using the three platforms and evaluated single nucleotide variants (SNVs), insertions/deletions (indels), and structural variants (SVs) detection, stratifying by high-complexity, low-complexity, and dark genome regions while assessing effects of multiplexing, depth, and read length. LRS SNV accuracy was slightly lower than that of SRS in high-complexity regions (F-measure: 0.954 vs. 0.967) but showed comparable sensitivity in low-complexity regions. LRS showed robust performance for small (1-5 bp) indels in high-complexity regions (F-measure: 0.869), but SRS agreement decreased significantly in low-complexity regions and for larger indel sizes. Within dark regions, LRS identified more indels than SRS, but showed lower base-level accuracy. LRS identified 2.86 times more SVs than SRS, excelling at detecting large variants (>6 kb), with SV detection improving with sequencing depth. Sequencing depth strongly influenced variant calling performance, whereas multiplexing effects were minimal. Our findings provide valuable insights for optimising LRS applications in genomic research and diagnostics.
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