insilicosv 0.0.6

Simulator of complex structural variants in genomes

insilicoSV (WIP): a framework for structural variant simulation

Overview

insilicoSV generates synthetic diploid genome sequences, given a reference genome and a configuration file.

It supports the following functionality:

• 19 types of structural variants (simple and complex), indels, and SNPs
• a grammar to define custom structural rearrangement signatures
• random, context-aware (e.g., in repeat regions), or fixed-mode genome placement

Installation

Prerequisite: Python 3.8 and up - Install

Installation using pip:

• $ pip install insilicosv

Installation using conda:

• Install and configure bioconda
• Install insilicosv with conda install insilicosv

To Run

The recommended workflow for running insilicoSV is as follows:

1. Create a new directory
2. Populate a simulation config file and place it in the directory
3. Run insilicoSV providing the config file as input:

insilicosv <config_yml>

4. Results will be produced in this directory

The config file syntax is detailed in the Input guidelines section of the documentation.

Documentation

For documentation outlining the different features of insilicoSV along with usage examples and data resources, please refer to the following sections:

• Input guidelines
• Example Use Cases
• SV Grammar
• Example SV Visualizations
• Tutorial Jupyter notebook

Authors

Chris Rohlicek - [e-mail]

Nick Jiang - [e-mail]

Ilya Shlyakhter - [e-mail]

Victoria Popic - [e-mail]