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. Edit and View Files w/ Nano
  8. Search and Manipulate Files (grep)
  9. Redirecting Standard Out
  10. Wildcards and Globbing
  11. Variables and parameter substitution
  12. .Bashrc
  13. File permissions
  14. Shell Scripts
  15. 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