A computational tool for simulation of viral synthetic integrations

This method provides the ability of fast simulation of viral synthetic integrations. SynTegra is implemented in C language, is flexible for multiple synthetic integration applications, and does not contain external dependencies. The tool accepts any sequences in FASTA format.

Installation

Conda

Install Miniconda, then run the following:

conda install -y -c bioconda syntegra

CMake via Git

Otherwise, CMake is needed for installation (http://www.cmake.org/). You can download it directly from http://www.cmake.org/cmake/resources/software.html or use an appropriate packet manager. If the system does not have cmake and git, please install it using the following

sudo apt-get install cmake git

After, the following instructions describe the procedure to install, compile and run SynTegra:

git clone https://github.com/cobilab/syntegra.git
cd syntegra/src/
cmake .
make

Execution

Run SynTegra

Run SynTegra tool with

SynTegra --host host.fa --virus virus.fa > out.fasta;

Parameters

To see the possible options type

SynTegra

or

SynTegra -h

Citation

On using this software/method please cite:

• pending

Issues

For any issue let us know at issues link.

License

GPL v3.

For more information:

http://www.gnu.org/licenses/gpl-3.0.html