Population Genomics of the Great Duckweed

The repository archives scripts involved in the great duckweed (Spirodela polyrhiza) population genomics project. The paper now can be found here: [link](https://www.nature.com/articles/s42003-024-06266-7)

Prerequisites

The scripts were written mainly using bash, Perl, Python and R, and calculations were done in an x86_64 GNU/Linux cluster. Please modify the running environment accordingly.

How to start

Before running the scripts, please download the raw data and store the "data" folder in the same directory where you put the "scripts" folder, like this:

• working_folder/
  • scripts/
    • Fig_1/
    • Fig_2/
    • ...
  • data/
    • Fig_1/
    • Fig_2/
    • ...

The tar.gz compressed folder of "data" could be downloaded here. Or, an alternative link: [10.5281/zenodo.14009270](https://doi.org/10.5281/zenodo.14009270)

Other files

Folder "S.polyrhiza_SpGA2022_annotation/" contains the updated S. polyrhiza genome annotation "SpGA2022".

Folder "Supplementary_data/" contains the supplementary data files involved in the duckweed_popg paper.