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Article

Accurate, Scalable Structural Variant Genotyping in Complex Genomes at Population Scales.

Molecular biology and evolution - 30 Jul 2025

Hu Ming, Wan Penglong, Chen Chengjie, Tang Shuyuan, Chen Jiahao, Wang Liang, Chakraborty Mahul, Zhou Yongfeng, Chen Jinfeng, Gaut Brandon S, Emerson J J, Liao Yi

Abstract excerpt

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 Structural Variants Genotyping of Assemblies on Population scales (SVGAP), a pipeline for...

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Topics

Genome, Plant
Genotyping Techniques
Zea mays
Genomic Structural Variation
Software
Phylogeny

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Identifiers

PMID: 40721218
DOI: 10.1093/molbev/msaf180
PMCID: PMC12362251

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