Notes for improvement (debrief 2023-11 course)

[tavareshugo]

• Technical issues
  • Mamba environments - need to double-check setup ahead of the course
• Need recap of Unix and sequencing on day 1 (maybe just 10 minutes of slides)
• Will use this repo to document the commands used during the course
• Exercises:
  • Going through manual page was really good practice
  • Maybe some practicals could involve the participants building the command themselves based on some hints and the help page.
• Open discussion exercises: these worked well in general
• We need some "candy" at the end of each day
  • more visualisation throughout the course
• The first discussion exercise was too open-ended (especially as they only had 1 lecture before it)
  • give a bit more guidance (slides with empty boxes like "controls", "collection method", etc.)
  • possibly using mentimeter and/or post-its on a board
  • have just one case study (based on a real project)
• Amplicon-based
  • went smoothly
  • Homework - worth checking if anyone managed to do this
• De novo metagenomics downstream analysis
  • include Hi-C in addition to binning
  • checkM and gtDB-tk are essential
  • phylogenetic tree with iTOL is useful as a motivational visualisation
  • other downstream analyses (AMR and gene annotation) can be mentioned but not covered
• Normalisation
  • add a slide for normalisation of read counts
• Interactive sessions - restrict to 1h

(at some point need to go through this issue and convert to actionable bullet points)