Snakemake Pipeline for Salmonella Genomics Analysis
Developed a reproducible computational workflow for large-scale genomic analysis of Salmonella enterica isolates to support surveillance, antimicrobial resistance profiling, and outbreak investigation.
My Contributions
- Designed and implemented a Snakemake workflow
- Automated genome assembly and quality control
- Managed Conda environments and SLURM jobs
- Performed downstream R analysis
- Generated AMR heatmaps and temporal visualizations
- Contributed to collaborative USDA-ARS report preparation
Tools Used
Snakemake R RStudio SLURM SPAdes SeqSero2 AMRFinderPlus QUAST MLST Conda Git
Project Report
Collaborative USDA-ARS and University of Georgia research project investigating genomic, epidemiological, and geospatial predictors of Salmonella outbreaks.
Code and Data
Featured Visualizations
AMR Gene Distribution Across Serovars
