Metabarcoding Pipeline

Metabarcoding Workflow

metabarcoding pipeline see text below

Metabarcoding Workflow (text version)

  1. Read Processing (DADA2)
    • Filtering and trimming
    • Error learning
    • Dereplication and denoising
    • Amplicon merging
    • Chimera removal
  2. Amplicon Sequence Variant (ASV) identification (dada2)
    • Taxonomic assignment (SILVA, but other possible)
    • Abundance quantification
  3. ASV analyses (Rmarkdown)
    • Contaminant removal (phyloseq + decontam)
    • Alpha diversity (vegan)
    • Beta diversity (vegan)
    • Composition and most abundant members (tidyverse)
    • Differential abundance (ANCOM-BC)