PAVFinder

PAVFinder detects structural variants, including gene fusions, in de novo assembled transcriptomes and genomes to support analysis of RNA sequencing data for cancer research and clinical diagnostics.

Key Features:

• Python package: Implemented in Python for computational analysis of assembled transcriptomes and genomes.
• De novo assembly compatibility: Compatible with de novo assemblies generated by ABySS and Trans-ABySS for analysis of complex transcriptome data.
• Structural variant and fusion detection: Identifies structural variants, including gene fusions, from assembled transcriptome and genome sequences.
• Integration with Fusion-Bloom: Serves as a component of the Fusion-Bloom method to combine de novo transcriptome assembly with assembly-based structural variant calling.
• Use of RNA-Bloom and assembly-based SV calling technologies: Incorporates RNA-Bloom and other assembly-based structural variant calling technologies to enhance fusion detection.

Scientific Applications:

• Cancer Research: Detection of gene fusions and structural variants relevant to cancer genomics studies.
• Clinical Diagnostics: Identification of clinically relevant gene fusions from RNA sequencing data to inform diagnostic and treatment decisions.

Methodology:

Leverages de novo transcriptome assembly and integrates with Fusion-Bloom (including RNA-Bloom) and assembly-based structural variant calling technologies to analyze RNA-seq data for structural variants and gene fusions.