Data Analysis - fastStructure Population Analysis of Oly GBS PyRAD Output

2016
Genotype-by-sequencing at BGI
fastStructure
jupyter notebook
olympia oyster
Ostrea lurida
Structure
Author

Sam White

Published

August 16, 2016

After some basal readings about what Fst is (see notebook below for a definition and reference), I decided to try to use fastStructure to analyze the PyRAD output from 20160727.

The quick, TL;DR: after spending a bunch of time installing the program, it doesn’t handle the default Structure file (.str); requires some companion file types that PyRAD doesn’t output.

I’ve put this here for posterity and background reference on Fst…

Will proceed with using the full blown Structure program to try to glean some info from these three populations.

Jupyter Notebook: 20160816_oly_gbs_fst_calcs.ipynb