ArticleGenome biology2021
A benchmark of structural variation detection by long reads through a realistic simulated model.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers, 1 of them a synthesis that pooled it.
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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
52 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Diagnostic yield of long-read sequencing for rare diseases: a systematic review.Frontiers in genetics · 2026Pooled it
- European ash pangenome reveals widespread structural variation and genetic basis of low ash dieback susceptibility.Nature communications · 2026Article
- Genomic Evidence of Early-Diverging Domesticated Lineages in Norwegian Farmhouse Yeast.Genome biology and evolution · 2026Article
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Dual-SVF: a robust knowledge-guided multimodal method for structural variant filtering in long-read sequencing.Briefings in bioinformatics · 2026Article
- DNA Replication Errors Drive Genome-Wide Small Inverted Triplication Dynamics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Large-scale human genomic resources drive innovations toward forensic intelligent source attribution and precision identification.International journal of legal medicine · 2026Review
- A review of computational approaches for metagenomics by long-read sequencing.Science China. Life sciences · 2026Review
- Article
- cuteHap: Haplotype-Aware Structural Variant Detection in Phased Long-Read Sequencing Data.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- NanoVar: a comprehensive workflow for structural variant detection to uncover the genome's hidden patterns.Nature protocols · 2026Review
- Bayesian Integrative Detection of Structural Variations With False Discovery Rate Control.Biometrical journal. Biometrische Zeitschrift · 2026Article
- A Murine Database of Structural Variants Identifies A Candidate Gene for a Spontaneous Murine Lymphoma Model.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Article
- Pangenomic structural variant patterns reflect evolutionary diversification in Brassica napus.Genome biology · 2025Article
- insilicoSV: a flexible grammar-based framework for structural variant simulation and placement.Bioinformatics (Oxford, England) · 2025Article
- OctopuSV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis.Bioinformatics (Oxford, England) · 2025Article
- Accurate, Scalable Structural Variant Genotyping in Complex Genomes at Population Scales.Molecular biology and evolution · 2025Article
- Review
- ConsensuSV-ONT - A modern method for accurate structural variant calling.Scientific reports · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accurate simulations of structural variation distributions and sequencing data are crucial for the development and benchmarking of new tools. We develop Sim-it, a straightforward tool for the simulation of both structural variation and long-read data. These simulations from Sim-it reveal the strengths and weaknesses for current available structural variation callers and long-read sequencing platforms. With these findings, we develop a new method (combiSV) that can combine the results from structural variation callers into a superior call set with increased recall and precision, which is also observed for the latest structural variation benchmark set developed by the GIAB Consortium.
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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 OpenQuestion graph.