ArticleNature communications2026
VACmap: an accurate long-read aligner for unraveling complex genomic rearrangements.
Article in Nature communications, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Clustering-based progressive alignment with fuzzy logic (CPA-FL).Biochemistry and biophysics reports · 2026Article
- VACmap: an accurate long-read aligner for unraveling complex genomic rearrangements.Nature communications · 2026Article
- Benchmark for simple and complex genome inversions.bioRxiv : the preprint server for biology · 2025Article
- Diploid donor-specific assembly enhances somatic structural variant detection in cancer genomes.bioRxiv : the preprint server for biology · 2025Article
- Gene-Pseudogene Inversions as a Hidden Source of Missing Heritability.medRxiv : the preprint server for health sciences · 2025Article
- A Hitchhiker's Guide to long-read genomic analysis.Genome research · 2025Review
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Sequence alignment is essential for genomic research and clinical diagnostics, yet detecting complex rearrangements such as inversions, duplications, and gene conversions remains challenging due to allele complexity and limitations of current methods. We introduce VACmap, a non-linear mapping approach to enhance the detection and representation of all genetic variations. VACmap improves duplication detection from 20% to 90% in the Challenging Medically-Relevant Genes (CMRG) benchmark and improves characterization of complex inversions in repetitive regions and gene conversion events. It improves resolving clinically significant loci, including the LPA gene (with repetitive KIV-2 units linked to coronary heart disease), GBA1 and STRC genes (risk factors for Parkinson's disease and hearing loss, respectively, affected by pseudogene recombination with GBAP1 and STRCP1). Here, we show that VACmap delivers better alignment accuracy and SV detection, providing a robust tool for genomic analysis and clinical insights, with potential to advance understanding of genetic diversity and disease mechanisms.
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Registered trials
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