This is the code to run the simulations for Hrystenko et al. 2022

MOST OF THE THIS CODE IS COPIED (and revised) FROM https://github.com/YanaHrytsenko/determining_population_structure_from_k-mer_frequencies

Open the .slim file in the SlimGUI and run it (did this on my Mac locally not a cluster)
Copy the output to a .fa file and delete the header text

Open 1_jellyfish.sh - edit this file where it says change and run
Repeat for 2_ and 3_ sh files

For the structure comparison in the paper:
Run get_snps.sh to convert fasta files to structure format using the python script - you need to manually change each file name
Run faststructure.sh to reun faststructure, manually observed best K and run distruct accordingly (commented out)

This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <https://www.gnu.org/licenses/>.