|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|
|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?
|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?
How can I search within files?
How can I combine existing commands to do new things?
|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?
|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?|
The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.