simuG

simuG simulates the full spectrum of genomic variants—including SNPs, INDELs, CNVs, inversions, and translocations—to generate benchmark genomes for evaluation of variant detection and analysis.

Key Features:

• Full-spectrum variant simulation: Simulates SNPs, INDELs, CNVs, inversions, and translocations as either predefined or random variants.
• Coding-partition SNP control: Simulates SNPs specifically in coding sites, noncoding sites, 4-fold degenerate sites, and 2-fold degenerate sites.
• CNV formation mechanisms: Simulates CNVs arising from segmental deletions, dispersed duplications, and tandem duplications.
• Breakpoint specificity: Simulates inversions and translocations with specified types of breakpoints.
• Organism-agnostic application: Applicable to any organism, with particular utility in human genomics research.

Scientific Applications:

• Benchmarking variant detection: Generates genomes with known variant configurations for benchmarking variant callers and downstream analyses.
• Analytical method evaluation: Provides controlled datasets for assessing the performance of bioinformatics tools and workflows in detecting and characterizing variants.
• Genetic research and evolutionary biology: Supplies simulated variant sets for studies in genetics and evolutionary analyses.
• Personalized medicine and computational genomics: Produces test data to support development and validation of methods in personalized medicine and computational genomics.

Methodology:

Implemented in Perl.