ALIBI - Algorithm for Linearization by Incremental graph BuIlding

Prerequisites

Running:

• Python 3
• Biopython

Installation

1. Clone this repository:

   git clone https://github.com/anialisiecka/ALIBI.git

2. Change directory:

   cd ALIBI

3. Run the setup.py file from that directory:

   python setup.py install

Input

ALIBI requires as input a GFA file (Graphical Fragment Assembly) or a MAF file (Multiple Alignment File) with a sequence graph.

Output

ALIBI linearizes the genome sequence graph present in the input file. The final linearized graph is written to a file of the same format as the input file.

Usage

To use ALIBI you need to be in the ALIBI folder.

bash alibi.sh -i <input_file>

The final linearized graph is written to a GFA or MAF file with the same name as the input file, but with "_sorted" suffix before the file extension.

Founding

This software is developed with support of OPUS 11 scientific project of National Science Centre: Incorporating genomic variation information into DNA sequencing data analysis.

License

This project is licensed under the MIT License - see the LICENSE file for details.