prewas manuscript analysis

This repository contains the data and R scripts in support of a manuscript submitted to biorxiv. The focus of this work is to assess the potential impact of SNP pre-processing choices on bGWAS results.

The preprint will be available soon on biorxiv.

Manuscript Title

prewas: Data pre-processing for more informative bacterial GWAS

Mansucript Authors

Katie Saund* (https://orcid.org/0000-0002-6214-6713), Zena Lapp* (https://orcid.org/0000-0003-4674-2176), Stephanie N. Thiede* (https://orcid.org/0000-0003-0173-4324), Ali Pirani (https://orcid.org/0000-0001-7810-0982), and Evan S. Snitkin (https://orcid.org/0000-0001-8409-278X)

*Equal contribution

Repository contents

This repository includes the R code necessary to generate the figures in the manuscript.
lib/plot_figures.R will use the data in data to plot the figures in figures.

Sequence data

All genome sequences available on NCBI (see Table S1).

Contributors

Katie Saund, Zena Lapp, and Stephanie N. Thiede all contributed code to this repository.

Citation

prewas: Data pre-processing for more informative bacterial GWAS
Katie Saund, Zena Lapp, Stephanie N. Thiede, Ali Pirani, Evan S Snitkin
bioRxiv 2019.12.20.873158; doi: https://doi.org/10.1101/2019.12.20.873158