Microbial Genomics Journey Workshop 2023

Instructor
Ahmed M. Moustafa

Teaching Assistants
Daniel P. Morreale (Dan)
Qianxuan She (Sean)
Erin Marie Theiller (Erin)

Recordings

All sessions were recorded and they are available on YouTube.

Syllabus

• Why is it important to learn microbial genomics?
• Aim
• Tips
• Knowledge Map
• Session 1: Unix
  • Why would I need to use command-line?
  • How to open a terminal?
    • Windows
    • Mac
  • Make a New Folder
  • Running Commands
  • Useful Unix Commands
  • Getting Information About Commands
  • Useful Command-Line Shortcuts and Keystrokes
  • Wildcards
  • Command Line Arguments
  • Standard Input and Output Redirection
  • GitHub
    • Make an account
    • Cloning a Repository
    • Updating a Local Repository
  • Conda
    • Install miniconda for Windows
    • Install miniconda for Mac
    • Install Mamba
  • Bioconda
    • Install FASTQC
    • Install MultiQC
    • Install Mash
    • Install Shovill
    • Install Quast
    • Install CheckM
    • Install Busco
    • Install Prokka
    • Install Bakta
    • Install abricate
    • Install mlst
  • Text Editors
  • Further Readings
• Problem Set 1
• Session 2: Quality Control
  • FASTA
  • FASTQ
  • Shotgun Metagenomics?!!
  • FASTQC
  • MultiQC
  • Mash
  • Further Readings
• Problem Set 2
• Session 3: Assembly
  • Intro
  • Shovill
  • Quast
  • Busco
  • Further Readings
• Problem Set 3
• Session 4: Annotation
  • Quality Check Summary
  • Intro
  • Prokka
  • abricate
  • Further Readings
• Problem Set 4
• Session 5: Blast database and Typing/MLST
  • Lecture by Dr. Kyle Bittinger
  • blast
  • mlst
  • SARS-CoV-2
  • Further Readings
• Problem Set 5
• Session 6: Reference based analysis
  • Decontaminate reads from phiX
  • Snippy
  • Further Readings
• Problem Set 6
• Session 7: Pangenome analysis
  • Roary
  • Panaroo
  • Scoary
  • Further Readings
• Problem Set 7
• Session 8: Panallelome analysis
  • WhatsGNU
  • Further Readings
• Problem Set 8
• Session 9: Metagenomics
  • Lecture by Dr. Ceylan Tanes
• Problem Set 9
• Session 10: Kmer analysis and Recombination Detection
  • Kmer analysis
    • PySeer
  • Recombination Detection
    • ClonalFrameML
  • Further Readings
• Problem Set 10
• Session 11: Phylogenetics
  • Lecture by Dr. Paul Planet
  • iqtree
  • Cladebreaker
  • Further Readings
• Problem Set 11
• Session 12: Workflows! What is next?
  • Feedback
  • Updated Knowledge Map
  • phastest
  • PlasmidFinder
  • geNomad
  • Nextflow
  • Snakemake
  • Programming for Biology
  • Further Readings
• Session 13: Graduation Project
  • Description
  • Solution
  • CHOP Cluster
  • Further Readings