| Name | insilicosv JSON |
| Version |
0.0.6
JSON |
| download |
| home_page | https://github.com/PopicLab/insilicoSV |
| Summary | Simulator of complex structural variants in genomes |
| upload_time | 2023-12-08 18:27:35 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.8 |
| license | MIT |
| keywords |
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
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| coveralls test coverage |
No coveralls.
|
# 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](https://www.python.org/downloads/)
Installation using pip:
* `$ pip install insilicosv`
Installation using conda:
* Install and configure [bioconda](https://bioconda.github.io/)
* 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](docs/input_guidelines.md) 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:
<!-- toc -->
- [Input guidelines](docs/input_guidelines.md)
- [Example Use Cases](docs/example_use_cases.md)
- [SV Grammar](docs/sv_grammar.md)
- [Example SV Visualizations](docs/example_sv_visualizations.md)
- [Tutorial Jupyter notebook](docs/demo_notebook.md)
## Authors
Chris Rohlicek - crohlice@broadinstitute.org
Nick Jiang - nickj@berkeley.edu
Ilya Shlyakhter - ilya@broadinstitute.org
Victoria Popic - vpopic@broadinstitute.org
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