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Welcome to the Wiki page for the "Ancient Environmental Genomics Course" – an immersive 6-day PhD course designed to equip you with the latest tools and knowledge for unraveling the mysteries of ancient environmental DNA. Whether your curiosity leads you to permafrost soils, lake sediments, ancient artifacts, dental plaque, fossilized excreta, ice samples, or other historical substrates, this course is your gateway to unlocking the secrets of the past.

Our primary objective is to empower you with the essential skills needed to decode the intricate web of DNA preserved in ancient environments. Throughout this course, you will delve into the world of taxonomic profiling, organelle and nuclear DNA placement, and learn to identify a diverse range of species, spanning from microbes to plants, animals, and even our own human ancestors.

Simply click on the respective day to access its content:

• Day 0

  • Access your workspaces
  • Connect to a Workspace
  • Using VS Code Web
  • Opening a Terminal
  • File Explorer, Search, and Command Palette
  • Install Other Extension
  • Using the R Extension
  • Course directory structure
  • Conda environments

• Day 1

  • Exercise 1
  • Exercise 2
  • Exercise 3
  • Exercise 4
  • Exercise 5
  • Exercise 6
  • Exercise 7
  • Exercise 8
  • Group assignment

• Day 2

  • Taxonomic classification
  • ngsLCA
  • Data-wrangling

• Day 3

  • Phylogenetic placement

• Day 4

  • Session 1
  • Session 2
  • Session 3
  • Session 4
  • Session 5
  • Session 6

• Day 5

  • Ancient pathogens
  • Group work
  • Presentations
  • Repo review and feedback

• Day ?

  • Lab tour