Metadata-Version: 2.1
Name: insilicosv
Version: 0.0.4
Summary: Simulator of complex structural variants in genomes
Home-page: https://github.com/PopicLab/insilicoSV
Author-email: Chris Rohlicek <crohlice@broadinstitute.org>, Nick Jiang <nickj@berkeley.edu>, Ilya Shlyakhter <ilya@broadinstitute.org>, Victoria Popic <vpopic@broadinstitute.org>
Project-URL: Homepage, https://github.com/PopicLab/insilicoSV
Project-URL: Issues, https://github.com/PopicLab/insilicoSV/issues
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
Requires-Dist: cycler
Requires-Dist: kiwisolver
Requires-Dist: matplotlib
Requires-Dist: numpy
Requires-Dist: Pillow
Requires-Dist: pyparsing
Requires-Dist: pysam
Requires-Dist: python-dateutil
Requires-Dist: PyYAML
Requires-Dist: six

# insilicoSV
insilicoSV is a software to design and simulate simple and complex structural variants, both novel and known. 

## Requirements  (Prerequisites)
* Python 3.6 and up - [Install](https://www.python.org/downloads/)

## Installation

`$ pip install -r requirements.txt`

## To Run
```
samtools faidx <ref.fna>   # if index file already produced, skip this line
python simulate.py <ref.fna> <par.yaml> <prefix>
```
**NB:** Before running will also need to set `PYTHONPATH` to point to the insilicoSV directory with `export PYTHONPATH={/path/to/insilicoSV}`

## Documentation
For documentation outlining the different features of insilicoSV along with usage examples and data resources, please refer to the wiki:
<!-- toc -->
- [Input guidelines](https://github.com/PopicLab/insilicoSV/wiki#input-guidelines)
- [Example Use Cases](https://github.com/PopicLab/insilicoSV/wiki#example-use-cases)
- [SV Grammar](https://github.com/PopicLab/insilicoSV/wiki/SV-Grammar)
- [Benchmark Genomes](https://github.com/PopicLab/insilicoSV/wiki/Benchmark-Genomes)
- [Automated Pipelines and Additional Utilities](https://github.com/PopicLab/insilicoSV/wiki/Automated-pipelines-and-additional-utilities)
- [Example SV Visualizations](https://github.com/PopicLab/insilicoSV/wiki/Example-SV-visualizations)


## Authors
Chris Rohlicek - crohlice@broadinstitute.org

Nick Jiang - nickj@berkeley.edu
