SimBA

SimBA evaluates and benchmarks RNA-Seq analysis pipelines for next-generation sequencing (NGS) data using simulated datasets to assess pipeline performance on predefined genomic incidents and mutations.

Key Features:

• Systematic Evaluation Methodology: Provides a structured framework to assess and compare RNA-Seq pipeline performance across specific biological questions.
• SimCT: Generates simulated RNA-Seq datasets that mimic real biological conditions and incorporate predefined genomic incidents and mutations.
• BenchCT: Compares pipeline outputs against the simulated variations to quantify accuracy and sensitivity in detecting the introduced events.
• Performance Insights: Identifies performance variability between tools and configurations and highlights benefits of combining outputs from multiple pipelines.

Scientific Applications:

• Genomic medicine benchmarking: Facilitates evaluation of RNA-Seq pipelines used to compare healthy and cancerous cells in translational and clinical research.
• Pipeline selection and optimization: Informs selection and configuration of bioinformatics tools for specific biological questions based on benchmarked performance.

Methodology:

The suite creates simulated datasets with SimCT that include predefined genomic incidents and mutations, then uses BenchCT to compare and quantify RNA-Seq pipeline outputs against those simulated benchmarks.