This project uses for loops in a parameterized Rmd that can subest SARS-CoV-2 Illumina short reads (PRJNA656695) by sample ID and datasheet on Linux host machines. I analyzed the short reads with R (dplyr, ggplot2).

This project is a practice of exploratory data analysis on White-tailed deer Illumina short reads (ID: PRJNA984950). The SARS-CoV-2 SNP variants found within different populations of White-tailed deer across the United States were called using sastQC, trimmomatic, BWA, and vcftools. My goal was to find what significance location had to SARS-CoV-2 variants through finding distribution of samples collected and seeing whether certain genes had more SNPs in certain states. I was also interested in if statewide SNP trends coincided with SNP trends in North Carolina and Massachusetts, two states where White-tailed deer may be a potential resevoir for SARS-Cov-2.