ArticleNature communications2023
Deciphering the exact breakpoints of structural variations using long sequencing reads with DeBreak.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed.
- SVPG: a pangenome-based structural variant detection approach and rapid augmentation of pangenome graphs with new samples.Nature methods · 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
- DNA Replication Errors Drive Genome-Wide Small Inverted Triplication Dynamics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Manual validation finds ultra-long-read sequencing best enables faithful, population-level structural variant calling in Drosophila melanogaster euchromatin with nanopore.G3 (Bethesda, Md.) · 2026Article
- gSV: a general structural variant detector using the third-generation sequencing data.Briefings in bioinformatics · 2026Article
- Telomere-to-telomere genome assembly of the wood tiger moth Arctia plantaginis.Scientific data · 2026Article
- cuteHap: Haplotype-Aware Structural Variant Detection in Phased Long-Read Sequencing Data.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Bayesian Integrative Detection of Structural Variations With False Discovery Rate Control.Biometrical journal. Biometrische Zeitschrift · 2026Article
- Population-level structural variant characterization using pangenome graphs.Nature genetics · 2026Article
- Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing.Nature biotechnology · 2026Article
- Benchmarking AlphaMissense against ClinVar for Diagnostic Interpretation of Missense Variants in Inherited Retinal Diseases.Ophthalmology science · 2026Article
- Challenges in the detection and assembly of virus integration structures in human genomes.Frontiers in oncology · 2026Review
- OctopuSV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis.Bioinformatics (Oxford, England) · 2025Article
- Mechanisms and genomic implications of break-induced replication.Nature structural & molecular biology · 2025Review
- A detailed guide to assessing genome assembly based on long-read sequencing data using Inspector.Nature protocols · 2025Review
- SDFA: a standardized decomposition format and toolkit for efficient analysis of structural variants in large-scale population genomic studies.Genome biology · 2025Article
- Article
- Accurate, Scalable Structural Variant Genotyping in Complex Genomes at Population Scales.Molecular biology and evolution · 2025Article
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Authors and funding
8 authors.
Funding
Abstract
Long-read sequencing has demonstrated great potential for characterizing all types of structural variations (SVs). However, existing algorithms have insufficient sensitivity and precision. To address these limitations, we present DeBreak, a computational method for comprehensive and accurate SV discovery. Based on alignment results, DeBreak employs a density-based approach for clustering SV candidates together with a local de novo assembly approach for reconstructing long insertions. A partial order alignment algorithm ensures precise SV breakpoints with single base-pair resolution, and a k-means clustering method can report multi-allele SV events. DeBreak outperforms existing tools on both simulated and real long-read sequencing data from both PacBio and Nanopore platforms. An important application of DeBreak is analyzing cancer genomes for potentially tumor-driving SVs. DeBreak can also be used for supplementing whole-genome assembly-based SV discovery.
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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.