ArticleBioinformatics (Oxford, England)2025
SVbyEye: a visual tool to characterize structural variation among whole-genome assemblies.
Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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55 citing papers in PubMed.
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- SynFlow: an interactive online genome structural variant viewer.Bioinformatics (Oxford, England) · 2026Article
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- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- Quantifying reference alignment bias in functional genomics analyses.Cell reports methods · 2026Article
- The howler monkey genome provides new insights into the distinctive howling and folivorous adaptations of New World monkeys.Genome biology · 2026Article
- Complex structural variation, phylogeny, and disease associations of the mucin pangenome.medRxiv : the preprint server for health sciences · 2026Article
- Segmentally Duplicated Regulatory Elements Undergo Human-Specific Rewiring.Molecular biology and evolution · 2026Article
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- The evolution of structural variation across 500 million years of vertebrate evolution.bioRxiv : the preprint server for biology · 2026Article
- The Vertebrate Genomes Project Phase I: A global reference genome resource.bioRxiv : the preprint server for biology · 2026Article
- Convergent evolution through independent rearrangements in the primate amylase locus.Cell reports · 2026Article
- Genetic diversity and regulatory features of human-specific NOTCH2NL duplications.Cell genomics · 2026Article
- Two melanic pigment patterns are associated with a sex chromosome-linked oncogene in the mountain swordtailbioRxiv : the preprint server for biology · 2026Article
- Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures.bioRxiv : the preprint server for biology · 2026Article
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Abstract
motivationWe are now in the era of being able to routinely generate highly contiguous (near telomere-to-telomere) genome assemblies of human and nonhuman species. Complex structural variation and regions of rapid evolutionary turnover are being discovered for the first time. Thus, efficient and informative visualization tools are needed to evaluate and directly observe structural differences between two or more genomes.
resultsWe developed SVbyEye, an open-source R package to visualize and annotate sequence-to-sequence alignments along with various functionalities to process these alignments. The tool facilitates the characterization of complex structural variants in the context of sequence homology helping resolve the mechanisms underlying their formation. AVAILABILITY AND IMPLEMENTATION: SVbyEye is available on GitHub (https://github.com/daewoooo/SVbyEye) and via Zenodo (https://doi.org/10.5281/zenodo.15303553).
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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.