This is a tool used to evaluate the alignment between an assembly graph, in the .gfa
format, and its reference, in the .fasta
or .fa
format.
- Operating system: Linux, including Ubuntu, RedHat, CentOS 7+, and others.
- Working Desktop Environment to render the GUI. This program won't function properly without it.
Known limitations
This tool can currently only be excecuted on a Linux
OS, due to a bug of graph-tool
package with macOS.
In order to execute the application:
- Install miniconda
- Clone this repo by either downloading the
.zip
and extracting it, or using thegit clone
command. - Open a terminal, navigate to the project folder and create a new conda environment:
This command should automatically install all required dependencies on the environment
cd /path/to/project/home/directory conda env create -f dependencies.yml
- Activate the newly created environment:
conda activate gaget
To launch the application run the following command inside the environment:
python GAGET.py -g path/to/graph/ -r path/to/reference
Additional options can be found using the --help
option:
python GAGET.py --help
or
python GAGET.py -h
python GAGET.py -g Test_Data/ebola_graph.gfa -r Test_Data/KM034562v1.fa