Section revisions

[tavareshugo]

Sections of materials that are ready to be moved to new documents:

• [x] Genomic surveillance
• [x] Intro to Unix
• [x] Basics of NGS
• [x] Preparing data
• [x] Quality of reads
  • Exercise: run mash on your data
• [x] Genome assembly
  • Exercise: run epi2me on your data
• [x] Quality of assembly
  • Exercise: run busco and checkM on your data
• [x] Sequence typing and phylogeny (pathogenwatch)
  • Exercise: load your data to pathogenwatch
• [x] Phylogenetic analysis (panaroo)
• [x] AMR
  • Exercise: run funcscan on your data
• [x] Reporting
  • Exercise: write a report for your samples

Case Study

• Public data to give example of analysis