Paleogenomics

Welcome to the 3rd edition of the “Physalia Paleogenomics” course, online version 16-20 November 2020.

Contents

• 1. List of Tools
• 2. Quality filtering of reads
  • 2.1. Reads quality control
  • 2.2. Reads quality filtering
• 3. Metagenomic screening of shotgun data
  • 3.1. Kraken
  • 3.2. Kraken2
  • 3.3. Mataphlan 3
• 4. Alignment of reads to a reference genome
  • 4.1. Preparation of the reference sequence
  • 4.2. Alignment of the reads to the reference sequence
  • 4.3. Create mapping summary reports
  • 4.4. Damage analysis and quality rescaling of the BAM file
  • 4.5. Edit Distance
• 5. Variant calling and visualization
  • 5.1. Variants calling
  • 5.2. Variants visualization
• 6. Filtering, annotating and combining SNPs
  • 6.1. SNPs filtering and annotion
  • 6.2. Compare and combine multiple annotation files
  • 6.3. Phylogenetic tree reconstruction
• 7. DO-IT-YOURSELF
• 8. R session
  • 8.1. Barplot
  • 8.2. UPGMA
  • 8.3. nMDS

Course overview

• Index
• Module Index
• Search Page