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SVbyEye: A visual tool to characterize structural variation among whole-genome assemblies
David Porubsky1, Xavi Guitart1, DongAhn Yoo1
1Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Biorxiv : the Preprint Server for Biology
|September 30, 2024
Summary
SVbyEye is a new R package for visualizing genome structural variations. It helps researchers understand complex genomic differences and their evolutionary impact by analyzing sequence alignments.
Area of Science:
- Genomics
- Bioinformatics
- Evolutionary Biology
Background:
- High-quality genome assemblies are now routinely generated for various species.
- Complex structural variations and rapid evolutionary changes are increasingly being discovered.
- There is a need for effective visualization tools to compare genome structures.
Purpose of the Study:
- To develop an open-source R package for visualizing and annotating sequence-to-sequence alignments.
- To facilitate the characterization of complex structural variants and their formation mechanisms.
Main Methods:
- Developed SVbyEye, an R package.
- Implemented functionalities to process alignments in PAF format.
- Enabled visualization and annotation of sequence alignments.
Main Results:
- SVbyEye allows for the evaluation of structural differences between multiple genomes.
- The tool aids in characterizing complex structural variants within homologous regions.
- It helps resolve the mechanisms underlying the formation of structural variations.
Conclusions:
- SVbyEye provides an efficient method for visualizing and analyzing genomic structural variations.
- The package supports the study of genome evolution and the resolution of complex structural differences.
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