Welcome to the Metabarcoding - QIIME2 workshop!

Contents:

• General Introduction
  • Objectives
  • Time and place
  • How to prepare?
    • Install QIIME2 version 2021.2
    • Familiarize yourself with UNIX
    • OPTIONAL: Sign up for the Crunchomics cluster
    • OPTIONAL: Become a member of the amplicomics group
• Getting started
  • The data package
  • Windows subsystem for Linux - users
  • How to use this tutorial?
    • Where to start
    • Activating your conda environment
    • Skipping steps
• Quality control and feature tabulation
  • Prepping the manifest file
  • Importing data
  • Primer removal
  • Feature table construction
    • Deblur denoise
    • DADA2 denoise
• Taxonomic classification
  • Importing the database
  • Extract reference reads
  • Train the classifier
  • Taxonomic classification
  • Taxonomic barplot
• Metabarcoding analyses on Crunchomics
  • Some preparatory steps
    • Setup your environment
    • Define global variables
    • Setup your working directory
  • Importing data
  • Primer removal
  • Feature table construction
    • Deblur denoise
    • DADA2-denoise
  • Taxonomic classification
    • Extract reference reads
    • Train the classifier
    • Taxonomic classification
    • Taxonomic barplot