Here you'll find the code associated with the paper:
Ament-Velásquez et al. (2024) High-quality genome assemblies of four members of the Podospora anserina species complex, Genome Biology and Evolution: evae034, https://doi.org/10.1093/gbe/evae034
The Snakemake pipelines follow this orde:
- 1_Annotation_v3 -- the de novo genome annotation with MAKER
- 2_FunctionalAnnotation -- functional annotation with Funannotate
- 3_CircosSppComplex -- Fig. 1
- 4_OrthoTrees -- Getting the single-copy orthologs
- 5_PodoPhylogeny -- the phylogenomic analyses for Fig. 2
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.
Disclaimer: These scripts and files are provided "as is" and without any express or implied warranties, including, without limitation, the implied warranties of merchantability and fitness for a particular purpose.