ArticleFrontiers in genetics2021
Evaluation of Germline Structural Variant Calling Methods for Nanopore Sequencing Data.
Article in Frontiers in genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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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.
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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.
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Who cites it
19 citing papers in PubMed.
- European ash pangenome reveals widespread structural variation and genetic basis of low ash dieback susceptibility.Nature communications · 2026Article
- Comprehensive evaluation of structural variation detection for germline and somatic analysis with long-read sequencing data.Briefings in bioinformatics · 2026Article
- SnakeBITE: A SNAKEmake-Based Interface for Third-Generation Sequencing Data Analysis.Biomolecules · 2026Article
- A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies.Biomedicines · 2025Article
- Systematic benchmarking of tools for structural variation detection using short- and long-read sequencing data in pigs.iScience · 2025Article
- Long-read structural and epigenetic profiling of a kidney tumor-matched sample with nanopore sequencing and optical genome mapping.NAR genomics and bioinformatics · 2025Article
- Leveraging long-read sequencing technologies for pharmacogenomic testing: applications, analytical strategies, challenges, and future perspectives.Frontiers in genetics · 2025Review
- Performance of somatic structural variant calling in lung cancer using Oxford Nanopore sequencing technology.BMC genomics · 2024Article
- Comprehensive and deep evaluation of structural variation detection pipelines with third-generation sequencing data.Genome biology · 2024Article
- Long-Read Structural and Epigenetic Profiling of a Kidney Tumor-Matched Sample with Nanopore Sequencing and Optical Genome Mapping.bioRxiv : the preprint server for biology · 2024Article
- Benchmarking long-read aligners and SV callers for structural variation detection in Oxford nanopore sequencing data.Scientific reports · 2024Article
- Long read sequencing on its way to the routine diagnostics of genetic diseases.Frontiers in genetics · 2024Review
- GASOLINE: detecting germline and somatic structural variants from long-reads data.Scientific reports · 2023Article
- AML with complex karyotype: extreme genomic complexity revealed by combined long-read sequencing and Hi-C technology.Blood advances · 2023Article
- Benchmarking Oxford Nanopore read alignment-based insertion and deletion detection in crop plant genomes.The plant genome · 2023Article
- Best Practices in Microbial Experimental Evolution: Using Reporters and Long-Read Sequencing to Identify Copy Number Variation in Experimental Evolution.Journal of molecular evolution · 2023Review
- Resolving complex structural variants via nanopore sequencing.Frontiers in genetics · 2023Review
- Construction of a trio-based structural variation panel utilizing activated T lymphocytes and long-read sequencing technology.Communications biology · 2022Article
- Comprehensive evaluation of structural variant genotyping methods based on long-read sequencing data.BMC genomics · 2022Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Structural variants (SVs) are genomic rearrangements that involve at least 50 nucleotides and are known to have a serious impact on human health. While prior short-read sequencing technologies have often proved inadequate for a comprehensive assessment of structural variation, more recent long reads from Oxford Nanopore Technologies have already been proven invaluable for the discovery of large SVs and hold the potential to facilitate the resolution of the full SV spectrum. With many long-read sequencing studies to follow, it is crucial to assess factors affecting current SV calling pipelines for nanopore sequencing data. In this brief research report, we evaluate and compare the performances of five long-read SV callers across four long-read aligners using both real and synthetic nanopore datasets. In particular, we focus on the effects of read alignment, sequencing coverage, and variant allele depth on the detection and genotyping of SVs of different types and size ranges and provide insights into precision and recall of SV callsets generated by integrating the various long-read aligners and SV callers. The computational pipeline we propose is publicly available at https://github.com/davidebolo1993/EViNCe and can be adjusted to further evaluate future nanopore sequencing datasets.
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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 Socratic graph.