ToTem

ToTem automates optimization of variant calling pipelines for next-generation sequencing (NGS) data to maximize precision, recall and overall variant-calling performance.

Key Features:

• Automated Pipeline Optimization: Automates generation, execution, and benchmarking of diverse variant calling pipeline configurations.
• Flexible Integration: Supports integration of nearly any bioinformatics tool or custom code and allows analyses to start at any pipeline stage.
• Cross-Validation Techniques: Employs cross-validation to prevent overfitting by penalizing precision, recall, and F-measure during validation.

Scientific Applications:

• Somatic variant calling from TGS: Optimizes somatic variant detection workflows for ultra-deep targeted gene sequencing (TGS) data.
• Germline variant detection in WGS: Optimizes germline variant calling workflows for whole genome sequencing (WGS) data.

Methodology:

Implemented in Java and PHP with a MySQL backend; performs automated generation, execution, and benchmarking of pipeline configurations and uses cross-validation that penalizes precision, recall, and F-measure.