This is a workflow that allows easily using a number of population structure analysis tools, with the goal to streamline workflows that allow easy comparison between methods and approaches. The original reason was to compare EEMS with other methods.
- EEMS
- flashpca
- admixture
- pong visualization of admixture
- TESS3
- treemix
- Spacemix
- conStruct
- FST (using plink)
Genotypic data is stored in plink format.
Metadata/location data is stored using John Novembre's
PopGenStructures
data format, with some minor (recommended) changes.
The pipeline is implemented using Snakemake,
using python
for most data wrangling and R
for most plotting
As some of the data used requires permission, we are not free to redistribute it. To re-generate all figures from the paper, it will be necessary to
- acquire access to all data and create master data set as described in the merge-pipeline
- change paths in
config/config.json
to reflect your working environment - run
snakemake all