MAGATT - Annotation transfert pipeline

MAGATT - Marker Assisted Gene Annotation Transfert for Triticeae

The MAGATT pipeline performs structural annotation transfert from a reference genome to a new target genome.

It uses ISBP markers designed as described in De Oliveira et al. (https://doi.org/10.3389%2Ffgene.2020.00891)  to guide BLAT alignments of each gene on the target genome.

It was used to re-annotate the IWGSC Reference Sequence of Chinese spring version 2.1 (https://doi.org/10.1111%2Ftpj.15289) and also to transfert the Chinese spring annotation to the new reference genome of wheat cv. Renan (https://doi.org/10.1093/gigascience/giac034).

The source code of the pipeline is available on the GitLab platform https://forgemia.inra.fr/umr-gdec/magatt

If you want to know more : https://umr-gdec.pages.mia.inra.fr/magatt