insilicosv 0.0.4

Simulator of complex structural variants in genomes

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

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:

• Input guidelines
• Example Use Cases
• SV Grammar
• Benchmark Genomes
• Automated Pipelines and Additional Utilities
• Example SV Visualizations

Authors

Chris Rohlicek - [e-mail]

Nick Jiang - [e-mail]