Paleogenomics at Tor Vergata

Tutorial of bioinformatics at the Laboratory of Molecular Anthropology, University of Rome Tor Vergata.

Contents

• 1. List of Tools
• 2. First step to set-up your machine
  • 2.1. Set-up your terminal machine
  • 2.2. Install Miniconda to work on your local machine
  • 2.3. Create an environment with Conda
  • 2.4. Install packages inside the environment
• 3. Useful commands
  • 3.1. Download FASTQ sequencing data from the SRA
  • 3.2. Download referece sequences from the NCBI
• 4. Working on HPC with Slurm
  • 4.1. Connect to the HPC cluster
  • 4.2. Run jobs with SLURM
• 5. Quality filtering of reads
  • 5.1. Reads quality control
  • 5.2. Reads quality filtering
• 6. Metagenomic screening of shotgun data
  • 6.1. Kraken 2
  • 6.2. Bracken
  • 6.3. Mataphlan 3
  • 6.4. Other tools
• 7. Alignment of reads to a reference genome
  • 7.1. Preparation of the reference sequence
  • 7.2. Alignment of the reads to the reference sequence
  • 7.3. Create mapping summary reports
  • 7.4. Alignment of reads to circular reference genomes
  • 7.5. Damage analysis and quality rescaling of the BAM file
  • 7.6. Edit Distance
• 8. Variant calling and visualization
  • 8.1. Variants calling
  • 8.2. Variants visualization
• 9. Filtering, annotating and combining SNPs
  • 9.1. SNPs filtering and annotion
  • 9.2. Compare and combine multiple annotation files
  • 9.3. Phylogenetic tree reconstruction
• 10. Analysis of Metagenomic data
  • 10.1. Prepare abundance tables for downstream analyses
  • 10.2. Sourcetracker
  • 10.3. Analyses with Phyloseq
• 11. Antimicrobial Resistance (AMR) analysis
  • 11.1. Build the CARD database
  • 11.2. Build the database of housekeeping (HK) genes
  • 11.3. Interrogate the CARD and Housekeeping genes databases
  • 11.4. Normalization of data
  • 11.5. AMR data analysis in R

• Index

• Module Index

• Search Page