TentacleSV

A Snakemake-based automated workflow for generating high-confidence structural variant (SV) call sets, powered by OctopusV. TentacleSV streamlines multi-caller SV analysis by integrating state-of-the-art callers with OctopusV's advanced BND correction and flexible merging capabilities.

🌟 Key Features

• Universal Input Support: Process both FASTQ files and pre-aligned BAM files
• Multi-platform Analysis: Comprehensive support for short-read and long-read sequencing data
• Automated Pipeline: From raw sequencing data to high-confidence SV call sets
• Powered by OctopusV: Advanced BND correction and flexible merging strategies

🔧 Supported Tools

Short-read Callers:

• Manta
• Delly
• Lumpy
• SVaba

Long-read Callers:

• CuteSV
• PBSV
• Sniffles2
• SVIM
• Debreak
• SVDSS

📦 Installation

# Clone the repository
git clone https://github.com/yourusername/TentacleSV.git
cd TentacleSV

# Create conda environment
mamba env create -f environment.yaml
conda activate tentaclesv

🚀 Quick Start

1. Configure Your Analysis

Edit config/config.yaml to specify your input data and parameters:

# For short-read data
seq_type: "short"
samples:
  sample1:
    type: "fastq"
    fq1: "path/to/R1.fastq.gz"
    fq2: "path/to/R2.fastq.gz"

# For long-read data
seq_type: "long_pacbio"  # or "long_ont"
samples:
  sample1:
    type: "fastq"
    fq1: "path/to/reads.fastq.gz"

2. Run the Pipeline

snakemake --cores 8 \
          --use-conda \
          --use-singularity \
          --singularity-args "--bind /projects,/home" \
          --conda-frontend mamba \
          --rerun-incomplete \
          --keep-going \
          -s workflow/Snakefile

📊 Output

TentacleSV generates:

• High-confidence SV call set (results/merged/{sample}.vcf)
• Quality metrics and logs
• Optional UpSet plots showing caller overlap

📄 Citation

If you use OctopusV or TentacleSV, please cite:

Guo Q, Li Y, Wang T, Ramakrishnan A, Yang R. OctopusV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis. bioRxiv. 2025. doi: 10.1101/2025.03.24.645012

📚 BibTeX

@article{guo2025octopusv,
  title={OctopusV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis},
  author={Guo, Qingxiang and Li, Yangyang and Wang, Tingyou and Ramakrishnan, Abhi and Yang, Rendong},
  journal={bioRxiv},
  year={2025},
  publisher={Cold Spring Harbor Laboratory},
  doi={10.1101/2025.03.24.645012},
  url={https://www.biorxiv.org/content/10.1101/2025.03.24.645012v1}
}

📄 License

This project is licensed under the MIT License - see the LICENSE file for details.

🤝 Contributing

Contributions are welcome! Please feel free to submit a Pull Request.