CAMPAREE

CAMPAREE simulates diploid RNA samples at the molecular level using empirical RNA data to produce realistic allele-specific and transcript-level molecule populations for evaluation and benchmarking of RNA-Seq analysis methods.

Key Features:

• Empirical Data Utilization: Uses empirical RNA data to produce simulated expression profiles that reflect observed biological conditions.
• Molecular-Level Simulation: Simulates RNA at the level of individual molecules and models heterogeneous transcript populations including degradation, splicing, and editing.
• Allele-Specific Data Generation: Generates allele-specific RNA data for diploid samples to represent expression differences between alleles.
• Modular Architecture: Separates input sample modeling from library preparation and sequencing processes to enable integration with different sequencing simulators.
• Adaptability to New Developments: Maintains sample and sequencing components independently to facilitate incorporation of new biological insights and sequencing technologies.

Scientific Applications:

• Idealized coverage plots: Produces coverage plots derived from real-data-based simulations for visualization and interpretation of RNA-Seq results.
• Benchmarking RNA-Seq methods: Provides realistic simulated datasets for benchmarking RNA-Seq analysis methods.
• Allelic expression studies: Supports allele-specific simulations for studies of genetic variation and allele-level expression differences.

Methodology:

Uses empirical RNA data to model diploid samples; simulates individual RNA molecules including degradation, splicing, and editing; and separates sample modeling from library preparation and sequencing components.