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Code to compare total genetic diversity in Humans vs Wheat

A word of warning

Almost all sequencing data is collected in a different way. I used an Ipython notebook (Data_munging.ipynb) to lightly munge the data before feeding it into a more consistent pipeline.

Analyzing the data is a set of functions with unit test calculating average entropy for a species with a number of individuals and a number of SNPs. uses these functions to calculated the analysis for wheat and humans. The wheat and human data comes in large csv files which must be downloaded separately hereand here

Plotting makes the pretty swarm plots. Note that it uses an inverse entropy calculation to approximate what a population of individuals with a given entropy score would look like. Granted, a single entropy score has a degenerate number of possible populations that could produce it, so I just found one solution that would work.


Code to compare total genetic diversity in Humans vs Wheat



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