OREI Teat Shotgun Metagenomics AMR Analysis

A repo dedicated to metegenome/resistome analyses of Shotgun sequencing of teat swabs of calving cows from four Farms, with some of the cows testing positive for Staphyloccocus aureus infection.

Analyses/Figures so far include:

• AMR Classification relative abundance barplot
• Principal Components Analysis (visualizing cow health statuses)
• PERMANOVA Testing
  • Days in Milk, S. aureus infection, Batch effects
• Time Series Differential Abundance (metagenomeseq) WIP
• AMR Differential Abundance Testing (ALDEX2)

 

Refer to OREI_Calfs_Report.pdf for Figures!