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.

It also takes as input an annotation file in GFF format, and the name of the genome related to the annotation (must be contained in the walks of the graph that correspond to this genome).

To run GrAnnoT you need to execute the file 'main.py'. The option '-h' will then descripe the inputs, outputs, and options available.

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