A tool designed to identify, reconstruct, and annotate complex structural variations—especially bridge-like translocations—from both second- and third- generation sequencing data. It integrates breakpoint clustering, graph-based modeling, and biological annotation to reveal intricate SV events that are often missed by traditional SV callers. CBSVB is particularly useful in cancer genome studies, where such rearrangements may indicate key pathogenic mechanisms.
Complex chromosomal rearrangements are central to the progression of many diseases, especially cancer. While well-known models such as chromothripsis have been extensively studied, less attention has been paid to patterns like bridge-like translocations — SVs that form via chained breakpoints connected by deletions or duplications. CBSVB aims to fill this gap.
- Both second- and third-generation sequencing data support: Optimized for PacBio/Nanopore data
- Graph-based integration: Connects and merges SV signatures using breakpoint graphs
- Bridge-like translocation detection: Identifies and annotates BLT structures automatically
Clone the repository and install dependencies:
git clone https://github.com/your-username/CBSVB.git
cd CBSVB
conda create --name cbsvb --file requirements.txt
conda activate cbsvb
python3 transer.py -o result -b [your bams' path] -seq_type [sequencing data type, 'hifi','ont' or 'ngs']| -o | OUTPUT PATH | Absolute path to output |
| -b | BAMS PATH | Absolute path to bam files |
| -seq_type | SEQ TYPE | The type of sequence, ngs or hifi or ont |python3 transer.py -o result -b [your bams' path] -seq_type [sequencing data type]