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 2
  • 3.2. Bracken
  • 3.3. Mataphlan 3
  • 3.4. Other tools
• 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
  • 7.1. Hands-on 1: ancient human mtDNA
  • 7.2. Hands-on 2: ancient human dental calculus
• 8. Material from previous courses
  • 8.1. Kraken

Course overview

• Index

• Module Index

• Search Page