Contact: Belson Malcolm Kutambe
Email: bkutambe@mlw.mw

This repository hosts Snakemake-based pipelines for genomics analysis of Salmonella Isangi nanopore data. The repository structure is as follows:

• envs
  
  • Contains the yaml environment configuration scripts.
• analysis scripts
  
  • Contains snakemake scripts for complete genome analysis
• polishing scripts
  
  • Contains snakemake scripts for genome polishing
• supplementary scripts
  
  • Contains bash scripts that act as helper scripts to organize directories in the pipelines,split files and generate workflows graphs.