SVIM-asm

SVIM-asm detects and genotypes structural variants in haploid and diploid genome assemblies to identify and phase deletions, insertions, tandem duplications, interspersed duplications, inversions, and other structural variant classes.

Key Features:

• Support for Haploid and Diploid Assemblies: Analyzes both haploid and diploid genome assemblies, including haplotype-resolved sequences.
• Detection of Multiple Variant Classes: Identifies six structural variant classes: deletions, insertions, tandem duplications, interspersed duplications, inversions, and additional classes not specified by other tools.
• High Sensitivity and Accuracy: Demonstrated higher sensitivity and F1 scores for insertions and deletions compared with DipCall on HG002 assemblies.
• Genotyping and Phasing Capability: Performs direct genotyping and phasing of structural variants to assign allelic states.
• Alignment Input: Operates on sorted BAM files, preferably generated using minimap2, to support genome-genome alignment-based SV detection.

Scientific Applications:

• Genomic Medicine: Improves detection of disease-associated structural variants through increased sensitivity and accuracy.
• Population Genetics: Enables genotyping and phasing of SVs for studies of genetic diversity and evolutionary history.
• Personalized Genomics: Supports comprehensive variant detection for individual genome characterization and interpretation.

Methodology:

Analyzes sorted BAM files, preferably generated using minimap2, to perform genome-genome alignments and identify and genotype structural variants between a query assembly and a reference genome.