Benchmarking, detection, and genotyping of structural variants in a population of whole-genome assemblies using the SVGAP pipeline.

ABSTRACT: Comparisons of complete genome assemblies offer a direct procedure for characterizing all genetic differences among them. However, existing tools are often limited to specific aligners or optimized for specific organisms, narrowing their applicability, particularly for large and repetitive plant genomes. Here, we introduce SVGAP, a pipeline for structural variant (SV) discovery, genotyping, and annotation from high-quality genome assemblies at the population level. Through extensive benchmarks using simulated SV datasets at individual, population, and phylogenetic contexts, we demonstrate that SVGAP performs favorably relative to existing tools in SV discovery. Additionally, SVGAP is one of the few tools to address the challenge of genotyping SVs within large assembled genome samples, and

SUBMITTER: Hu M 

PROVIDER: S-EPMC11839052 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature