Development notes

[tavareshugo]

Case study markdown

We can do something similar to the SARS workshop, where we outline a "case study" that goes through the analysis from start to finish.

Here is an outline draft:

• Setting up directories and Preparing files (samplesheet, metadata)
• Assembly (epi2me/wf-bacterial-genomics)
• Assembly quality - is it Vibrio cholerae?
  • Genome coverage (epi2me, CheckM)
  • Completeness (BUSCO, CheckM)
  • Contamination (CheckM, MASH)
• Typing - is it a pathogenic strain (7PET)?
  • epi2me reports already indicates this
  • Run Pathogenwatch to check if samples cluster with ST69
  • cgMLST (possibly can be done within Pathogenwatch)
  • Phylogenetic analysis using public sequences
• AMR
  • Reports from Pathogenwatch
  • nf-core/funcscan to run a more complete analysis
• Write a report
  • Could use GDoc template to start with
  • If we have time, could provide a R script/markdown to build automatic report

Slides

These can be done after the case study is drafted, as they should complement the concepts needed to make progress during the analysis.

• AMR slides - Andries will do these
• Phylogenetic intro - possibly Katy can adapt her slides used for SARS

Misc

TODO

• Instructor guidelines
• Instructions for participants:
  • Create an account on epi2me
  • Attend Unix pre-session (Zoom)
  • Fill-in Unix/R knowledge survey
• Make a GSite
• Survey of Unix/R knowledge