This repo contains scripts related to the preprint entitled "Rapid and repeatable genome evolution across three hybrid ant populations" available on bioRxiv.
The folder reads2SNPs contains scripts for trimming, mapping and deduplicating reads, and then calling, filtering and phasing variant sites (check the preprint for software versions). Note the script 7_SNP_calling_4pixy.sh performs variant and invariant site calling to estimate diversity & divergence metrics in 20kb windows with pixy.
The folder local_ancestry contains scripts to perform local ancestry inference using Loter, topology weighting with Twisst and good old chromosome painting.
The folder simulations contains scripts to run coalescent admixture simulations under single origin (SO, two hybrid populations arose though a unique admixture event) or independent origins (IO, each hybrid population arose through one admixture event) scenarios using msprime. The script example.sh runs 100 simulations for the LanW-LanR population pair under a SO scenario (LanWLanR_SO.py script) as a Slurm array job.