Scripts and Snakemake pipelines associated with the paper of Ament-Velásquez et al. "Allorecognition genes drive reproductive isolation in Podospora anserina", Nature Ecology & Evolution.
There are three main Snakemake pipelines. The first one, SNPpop.smk, must be run first. Some of the outputs are used by the other two pipelines. So, the order goes:
1 - SNPpop.smk
2 - DiversityStats.smk
3 - PaLD.smk
Each pipeline in turn depends on a small conda environment(s), as explained in their own README files.
As output of all the pipelines there is a results folder that usually contains the figures used in the paper.
I ran the pipelines in Uppsala University's supercomputer UPPMAX, which has a CentOS Linux operating system with a slurm scheduler. However, they should work fine also in other unix environments.
There are two scripts that are not part of the Snakemake pipelines: DiversityStats/scripts/PaEcology.R and MutantsFertility/scripts/PaMutantsFertility.R. They have to be run manually and require the input and output names to be changed in order to work!
In addition to the bioinformatic pipelines, the folder SLiMsimulations contains the code and simulations using SLiM 3 written by Ivain Martinossi.