COVID-19 Information

Bioinformatics Modules

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I. Introduction:

  1. Introduction to Genomics and Bioinformatics modules
  2. Principles of genomics
  3. Generation of genomic data: NGS sequencing
  4. Data structures and conventions
  5. Sequencing and assembling a genome
  6. Genome annotation and inferring function

II. Getting started

  1. Logging onto the Server

III. “Command Line” tools:

  1. Anatomy of a Command
  2. Finding Help
  3. Pathways and Directories
  4. Moving About
  5. Move, Copy and Delete
  6. Odds and Ends
  7. Using Nano
  8. Viewing Files
  9. Grep
  10. Redirecting Standard Out
  11. Wildcards and Globbing
  12. Variables and parameter substitution
  13. .Bashrc
  14. File permissions
  15. Shell Scripts
  16. Nohup

IV. Assembling and annotating a genome:

  1. Trimmomatic: Data QC
  2. SPADeS: assembling a genome
  3. QUAST: assembly Metrics
  4. Prokka: Annotating a genome