Bioinformatics Video Tutorials

There are many of the video tutorials, but they are short.  Most of them involve active participation so they need to be logged onto the server to follow along.

  1. Students can start with the  Introductory videos.  They should view them in order.
  2. Next, they should view the video on how to log into the server.  This is critical because the rest of the videos require that they follow along.
  3. Then work thru the videos from the top of the list down.
  4. Toward the end the videos include instructions on how to analyze their data.
  1. 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
  2. Getting started:
    1. Logging onto the Server
  3. “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. Text Editing Without nano
    9. Grep
    10. Pipes and redirecting
    11. Globbing and Wildcards
    12. Variables and parameter substitution
    13. Configuration
    14. File permissions
    15. Shell Scripts
    16. Nohup
    17. Transparency and reproducibility (in process)
  4. Assembling and annotating a genome:
    1. Trimmomatic: Data QC
    2. SPADeS: assembling a genome
    3. QUAST: assembly Metrics
    4. Prokka: Annotating a genome
    5. Making your data public (in process)
    6. Publishing your Microbial genome (in process)
  5. Exploring your Microbe
    1. Blast taxonomy
    2. Getting data
    3. File transfer
    4. Quast reference
    5. Orthofinder Part 1
    6. Orthofinder Part 2