GrAnnoT is an annotation transfer tool for pangenome graphs. It can transfer genome annotations to a pangenome graph containing the genome, and also transfer the pangenome graph's annotations on the genomes it contains.
GrAnnoT is an annotation transfer tool for pangenome graphs. It can transfer genome annotations to a pangenome graph containing the genome, and also transfer the pangenome graph's annotations on the genomes it contains.
This project is young and in development, some errors will be corrected, improvements will be made and new features will appear in the near future.
This project is young and in development, some errors will be corrected, improvements will be made and new features will appear in the near future.
## Usage
## Usage
GrAnnoT requires the graph to be in GFA format with W-lines that describe the walks of the input genomes. For example minigraph-cactus gives that kind of output.
GrAnnoT requires the graph to be in GFA format with W-lines that describe the walks of the input genomes. For example minigraph-cactus gives that kind of output.
You first need to extract from the GFA the positions of the segments of the graph on the genomes it contains. For this you need to run the script getSegmentsCoordinates.py with the GFA file as input.
You first need to extract from the GFA the positions of the segments of the graph on the genomes it contains. For this you need to run the script getSegmentsCoordinates.py with the GFA file as input.
