MIRACUM-Pipe

MIRACUM-Pipe provides end-to-end processing and analysis of next-generation sequencing (NGS) data for somatic variant detection, copy number variation estimation, RNA fusion detection, complex biomarker evaluation, annotation, visualization, and clinical interpretation in oncology.

Key Features:

• Workflow integration: Integrates multiple individual bioinformatics tools into a unified pipeline covering successive NGS data processing stages.
• Quality control: Implements quality control measures for raw sequencing data.
• Read alignment: Performs alignment of sequencing reads.
• Variant calling: Conducts somatic variant calling on aligned NGS data.
• Copy number variation estimation: Estimates copy number variations from sequencing data.
• RNA fusion detection: Detects RNA fusions from transcriptomic sequencing data.
• Complex biomarker evaluation: Evaluates complex biomarkers relevant to tumor biology.
• Annotation: Provides comprehensive annotation of variants and genomic alterations.
• Visualization and interactive reporting: Generates visual outputs and interactive reports for interpretation of genomic results.
• Standardized and customizable workflows: Offers a standardized pipeline architecture with options for customization to specific analyses.

Scientific Applications:

• Oncology research: Enables analysis of tumor genomes to study genomic alterations and biomarkers.
• Molecular Tumor Boards: Supports interpretation of somatic variants and genomic alterations in multidisciplinary clinical review settings.
• Precision oncology: Supports identification of actionable variants and biomarkers to inform targeted therapies and personalized treatment decisions.

Methodology:

Integration of multiple tools into a cohesive workflow performing quality control, read alignment, somatic variant calling, copy number variation estimation, RNA fusion detection, complex biomarker evaluation, variant annotation, and generation of visual outputs and interactive reports.