This is the repository for all the codes used for the EU-JRC funded MedBlueSGen project and from the paper by Leone et al., 2023:
Leone, A., Arnaud-Haond, S., Babbucci, M., Bargelloni, L., Coscia, I., Damalas, D., Delord, C., Franch, R., Garibaldi, F., Macias, D., Mariani, S., Martinsohn, J., Megalofonou, P., Micarelli, P., Nikolic, N., Prodöhl, P.A., Sperone, E., Stagioni, M., Zanzi, A., Cariani, A., Tinti, F. (2024). Population genomics of the blue shark, Prionace glauca, reveals different populations in the Mediterranean Sea and the North East Atlantic. Evolutionary Applications, 17(9): e70005. doi: https://doi.org/10.1111/eva.70005
An interactive sampling map is available here
After optimized assembly and SNPs calling, the dataset has been filtered using many criteria.
dDocent steps and filtering can be found here
The Rmarkdown file with post dDocent steps and Population Genetics analysis can be found here
