ArticleNature methods2023
SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads.
Article in Nature methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 32 citations in OpenAlex.
- Structural variant detection across sequencing technologies.Nature biotechnology · 2026Article
- dicast: a machine learning method for accurate structural variant detection from short-read sequencing data.Genome biology · 2026Article
- Comprehensive evaluation of structural variation detection for germline and somatic analysis with long-read sequencing data.Briefings in bioinformatics · 2026Article
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- gSV: a general structural variant detector using the third-generation sequencing data.Briefings in bioinformatics · 2026Article
- cuteHap: Haplotype-Aware Structural Variant Detection in Phased Long-Read Sequencing Data.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Population-level structural variant characterization using pangenome graphs.Nature genetics · 2026Article
- bronko: ultrafast, alignment-free detection of viral genome variation.bioRxiv : the preprint server for biology · 2026Article
- Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing.Nature biotechnology · 2026Article
- OctopuSV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis.Bioinformatics (Oxford, England) · 2025Article
- Comprehensive benchmarking of somatic structural variant detection at ultra-low allele fractions.bioRxiv : the preprint server for biology · 2025Article
- TRsv: simultaneous detection of tandem repeat variations, structural variations, and short indels using long read sequencing data.Genome biology · 2025Article
- Accurate, Scalable Structural Variant Genotyping in Complex Genomes at Population Scales.Molecular biology and evolution · 2025Article
- Review
- Benchmarking, detection, and genotyping of structural variants in a population of whole-genome assemblies using the SVGAP pipeline.bioRxiv : the preprint server for biology · 2025Article
- De novo and somatic structural variant discovery with SVision-pro.Nature biotechnology · 2025Article
- Challenges in structural variant calling in low-complexity regions.GigaScience · 2025Article
- ASVBM: Structural variant benchmarking with local joint analysis for multiple callsets.Computational and structural biotechnology journal · 2025Article
- VolcanoSV enables accurate and robust structural variant calling in diploid genomes from single-molecule long read sequencing.Nature communications · 2024Article
- SVDF: enhancing structural variation detect from long-read sequencing via automatic filtering strategies.Briefings in bioinformatics · 2024Article
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Authors and funding
5 authors at 4 institutions in 3 countries.
Funding
Abstract
Structural variants (SVs) account for a large amount of sequence variability across genomes and play an important role in human genomics and precision medicine. Despite intense efforts over the years, the discovery of SVs in individuals remains challenging due to the diploid and highly repetitive structure of the human genome, and by the presence of SVs that vastly exceed sequencing read lengths. However, the recent introduction of low-error long-read sequencing technologies such as PacBio HiFi may finally enable these barriers to be overcome. Here we present SV discovery with sample-specific strings (SVDSS)-a method for discovery of SVs from long-read sequencing technologies (for example, PacBio HiFi) that combines and effectively leverages mapping-free, mapping-based and assembly-based methodologies for overall superior SV discovery performance. Our experiments on several human samples show that SVDSS outperforms state-of-the-art mapping-based methods for discovery of insertion and deletion SVs in PacBio HiFi reads and achieves notable improvements in calling SVs in repetitive regions of the genome.
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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.