Microbiome tutorial 2020

Bioinformatik, Medical Life Science - WS 2019/2020 @CAU

Authors: Lucas Moitinho-Silva (l.silva@ikmb.uni-kiel.de), Malte Rühlemann (m.ruehlemann@ikmb.uni-kiel.de)

Includes data and scripts to guide you from raw amplicon data processing to diversity analysis.

Requires

Tutorial performed on a:

• R version 3.6.3 (2020-02-29)
• Platform: x86_64-pc-linux-gnu (64-bit)
• Running under: Ubuntu 18.04.5 LTS

with main packages:

• dada2_1.12.1
• phyloseq_1.28.0
• tidyverse_1.2.1
• vegan_2.5-5
• microbiome_1.11.2
• DESeq2_1.24.0

References

This material was based on phyloseq tutorials, including the Bioconductor workflow for microbiome data analysis