This repository contains the NGS pipeline used for the second chapter of my M.Sc. thesis. Note that this is the pipeline ONLY, and does not include any further statistical analysis.

The data from this pipeline are publically available from the National Center for Biotechnology Information database, under the project ID: PRJNA297448.

This project relies heavily on python coding expertise, and incorporates several github .py shells from other users. Credit for these additional shells are given in the Illumina-pipeline.py script.

Complete analysis for this project can be found in my M.Sc. thesis and several published manuscripts.

• Bobbie, Colleen Bridget. Linking fitness and the microbiota: exploring variation in microbial composition in the North American red squirrel (Tamiasciurus hudsonicus). Diss. Laurentian University of Sudbury, 2015.

• Stothart, Mason R., et al. "Stress and the microbiome: linking glucocorticoids to bacterial community dynamics in wild red squirrels." Biology letters 12.1 (2016): 20150875.

• Bobbie, Colleen B., Nadia Mykytczuk, and Albrecht I. Schulte-Hostedde. "Temporal variation of the microbiome is dependent on body region in a wild mammal (Tamiasciurus hudsonicus)." FEMS Microbiology Ecology 93.7 (2017).