Running:
- Clone this repository:
git clone https://github.com/anialisiecka/ALIBI.git
- Change directory:
cd ALIBI
- Run the setup.py file from that directory:
python setup.py install
ALIBI requires as input a GFA file (Graphical Fragment Assembly) or a MAF file (Multiple Alignment File) with a sequence graph.
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.
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.
This software is developed with support of OPUS 11 scientific project of National Science Centre: Incorporating genomic variation information into DNA sequencing data analysis.
This project is licensed under the MIT License - see the LICENSE file for details.