Metagenomic analysis of NGS data

Tutorial of bioinformatics for the metagenomic analysis of Next-Generation Sequencing data. Course of the PhD school in Ecology and Evolutionary Biology at the University of Rome Tor Vergata.

Contents

• 1. Course material
  • 1.1. List of Tools
  • 1.2. Datasets to download
• 2. Quality filtering of reads
  • 2.1. Reads quality control
  • 2.2. Reads quality filtering
• 3. Metagenomic screening of shotgun data
  • 3.1. Kraken2
  • 3.2. Bracken
  • 3.3. Mataphlan 3
  • 3.4. Other tools
• 4. Prepare abundance tables for downstream analyses
  • 4.1. Parse the kraken/bracken outputs to abundance tables
  • 4.2. Normalization of the abundance table for genome length
  • 4.3. Retrieve full taxonomic ranks of the abundance table
• 5. Analysis of Metagenomic data in R
  • 5.1. Install R packages
  • 5.2. Importing abundance tables in Phyloseq
  • 5.3. Barplot of taxa abundances
  • 5.4. Alpha diversity
  • 5.5. Note on compositional data
  • 5.6. Principal Coordinate Analysis (Multidimensional Scaling)
  • 5.7. Non-Metric Multidimensional Scaling
  • 5.8. Differential taxonomic abundances with DESeq2
  • 5.9. Principal Component Analysis (PCA)
• 6. Do it yourself
  • 6.1. Hands-on 1: Run the metagenomic analysis on a different dataset
  • 6.2. Hands-on 2: Run Kraken2 on an ancient dental calculus dataset

• Index

• Module Index

• Search Page