# SuperSeeker Pipeline
The SuperSeeker pipeline is a Python library for identifying subclonal evolution in cancer. It integrates various tools and scripts to process VCF files, cluster variants using PyClone-VI, and reconstruct subclonal evolutionary trees using SuperSeeker.
## Installation
### Step 1: Install External Tools
#### Installing PyClone-VI
PyClone-VI is used for clustering genetic variants. You can install it using Conda:
```bash
conda install -c bioconda pyclone-vi
```
#### Installing SuperSeeker
SuperSeeker is used for reconstructing the evolutionary history of subclones. You can install it from its source repository:
```bash
git clone https://github.com/yiq/SuperSeeker.git
cd SuperSeeker
```
Use the `requirements.txt` file to install the necessary Python packages:
```bash
pip install -r requirements.txt
```
### Step 3: Install the SuperSeeker Python Package
Finally, install the SuperSeeker Pipeline Python package:
```bash
pip install superseeker_pipeline
```
## Usage
To use the SuperSeeker pipeline, you can run the `run_pipeline` function from the `superseeker.pipeline` module. Here's an example:
```python
from superseeker.pipeline import run_pipeline
run_pipeline(
patient='patient1',
vcf_file='input_file.vcf',
patient_sex='M',
restarts=100,
clusters=10,
cn_neutral=True
)
```
## License
This project is licensed under the MIT License - see the [LICENSE.txt](LICENSE.txt) file for details.
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"description": "\n# SuperSeeker Pipeline\n\nThe SuperSeeker pipeline is a Python library for identifying subclonal evolution in cancer. It integrates various tools and scripts to process VCF files, cluster variants using PyClone-VI, and reconstruct subclonal evolutionary trees using SuperSeeker.\n\n## Installation\n\n### Step 1: Install External Tools\n\n#### Installing PyClone-VI\n\nPyClone-VI is used for clustering genetic variants. You can install it using Conda:\n\n```bash\nconda install -c bioconda pyclone-vi\n```\n\n#### Installing SuperSeeker\n\nSuperSeeker is used for reconstructing the evolutionary history of subclones. You can install it from its source repository:\n\n```bash\ngit clone https://github.com/yiq/SuperSeeker.git\ncd SuperSeeker\n```\n\nUse the `requirements.txt` file to install the necessary Python packages:\n\n```bash\npip install -r requirements.txt\n```\n\n### Step 3: Install the SuperSeeker Python Package\n\nFinally, install the SuperSeeker Pipeline Python package:\n\n```bash\npip install superseeker_pipeline\n```\n## Usage\n\nTo use the SuperSeeker pipeline, you can run the `run_pipeline` function from the `superseeker.pipeline` module. Here's an example:\n\n```python\nfrom superseeker.pipeline import run_pipeline\n\nrun_pipeline(\n patient='patient1',\n vcf_file='input_file.vcf',\n patient_sex='M',\n restarts=100,\n clusters=10,\n cn_neutral=True\n)\n```\n\n## License\n\nThis project is licensed under the MIT License - see the [LICENSE.txt](LICENSE.txt) file for details.\n",
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