Here you'll find the scripts and pipelines associated to the study Ament-Velásquez, Tuovinen, et al. (2020). The plot thickens: Haploid and triploid-like thalli, hybridization, and biased mating type ratios in Letharia. Front. Fungal Biol. 2:656386.
There are four main folders:
- MAT annotation: gene annotation of the MAT locus of the genus Letharia, designed to run in UPPMAX (Uppsala Multidisciplinary Center for Advanced Computational Science).
- Lichen Ploidy: a Snakemake pipeline to infer the ploidy (sensu lato, since it would include heterokaryosis) from a (meta)genome, as well as additional analysis to show that the triploid-like samples look like hybrids.
- Lichen Twisst: a snakemake pipeline where I make little trees of SNP windows along the main contigs of the L. lupina pure culture. The format is inspired in Twisst (Martin & Van Belleghem 2017 Genetics 206:429–438) for plotting but it's not at all as complicated.
- OtherFigures script and data necessary for other figures, mostly related to the repeat content.