README.md

Rarefaction of microbiome data

🎓 Guest speaker

• Dr Matteo Calgaro University of Verona, Italy

📙 Handsout:

• Rarefaction Practice in Microbiome Data Analysis

📃 Bibliography:

• Paul J. McMurdie, Susan Holmes: Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
• Pat Schloss: Waste not, want not: Revisiting the analysis that called into question the practice of rarefaction

📁 Data files in this directory:

• Output of 16S analysis of MiSeq SOP dataset using Dadaist2
  • feature table
  • taxonomy table
  • metadata
  • representative sequences
  • tree

# Download Silva 138 with `dadaist2-getdb` first
dadaist2 -r ~/refs/silva_nr_v138_train_set.fa.gz \
  -i MiSeq_SOP/ -m metadata.csv \
  -o dadaist2-output/ \
  --threads 16