| Setup | Download files required for the lesson | ||
| Day 1 | 00:00 | 1. Data Tidiness | How to collect and structure the data about your sequencing data |
| 00:30 | 2. Planning for NGS Projects | How to plan and organize your data for a genome sequencing project | |
| 01:00 | 3. Examining Data on the NCBI SRA Database | How to work with public data in the NCBI SRA | |
| 01:30 | Finish | ||
| Day 2 | 00:00 | 4. Introducing the Shell |
What is a command shell and why would I use one?
How can I move around on my computer? How can I see what files and directories I have? How can I specify the location of a file or directory on my computer? |
| 00:30 | 5. Navigating Files and Directories |
How can I perform operations on files outside of my working directory?
What are some navigational shortcuts I can use to make my work more efficient? |
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| 01:20 | 6. Working with Files and Directories |
How can I view and search file contents?
How can I create, copy and delete files and directories? How can I control who has permission to modify a file? How can I repeat recently used commands? |
|
| 02:05 | 7. Redirection |
How can I search within files?
How can I combine existing commands to do new things? |
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| 02:50 | 8. Writing Scripts | How can we automate a commonly used set of commands? | |
| 03:30 | 9. Project Organization |
How can I organize my file system for a new bioinformatics project?
How can I document my work? |
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| 04:00 | Finish | ||
| Day 3 | 00:00 | 10. Assessing Read Quality | How can I describe the quality of my data? |
| 00:50 | 11. Trimming and Filtering | How can I get rid of sequence data that doesn’t meet my quality standards? | |
| 01:45 | 12. Variant Calling Workflow | How do I find sequence variants between my samples and a reference genome? | |
| 02:45 | 13. Automating a Variant Calling Workflow | How can I make my workflow more efficient and less error-prone? | |
| 03:30 | Finish |
The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.