GrAnnoT

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. It also outputs complementary information such as the alignments of the transfered genes, or a presence-absence matrix.

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

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 can run GrAnnoT via the script main.py with the following arguments :

• GFA file with walks
• annotation file of a genome embedded in the graph
• the name of the source genome, that the annotation file refers to
• optionnaly the names of the target genomes (these names must be included in the walks of the graph). If no name is specified, the annotation will be transfered on all the genomes in the graph.

The other options can be found if you run "main.py -h".

It can output the following files :

For the graph :

• a GFF and a GAF file with the annotation of the graph

For each target genome :

• the GFF file with the annotation of the target genome
• a text file with the details of the variations within the annotated regions
• a text file with the alignments of the genes from the source genome and from the target genome

Support

If you have any question or suggestion, feel free to contact me by email : nina.marthe@ird.fr

Authors

If you use this program please cite Nina Marthe, Francois Sabot and Matthias Zytnicki.

MIT License