GAGET - Genome Assembly Graph Evaluation Toolkit

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.

System requirements

• 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.

Setup the environment

In order to execute the application:

1. Install miniconda
2. Clone this repo by either downloading the .zip and extracting it, or using the git clone command.
3. Open a terminal, navigate to the project folder and create a new conda environment:

   cd /path/to/project/home/directory
   conda env create -f dependencies.yml

   This command should automatically install all required dependencies on the environment
4. Activate the newly created environment:

   conda activate gaget

Excecute the software

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

Example execution

python GAGET.py -g Test_Data/ebola_graph.gfa -r Test_Data/KM034562v1.fa