This lesson uses the Software Carpentry and Data Carpentry lesson template and is inspired and partially based on the Data Carpentry Genomics lesson.
Schedule computer practical
- Tuesday, 9.30 - 12.15: Intro to data and the command line, downloading data
- Tuesday, 13.45 - 17.00: Trimming, SNP-based phylogeny, assembly
- Wednesday, 9.30 - 12.15: Visualizations, conclusions
This computer practical uses data from this publication We are using this collaborative document. A cheat sheet of the used Linux commands is available.
|Setup||Download files required for the lesson|
What are the goals of this practical training?
What data do we work on?
|00:20||2. Logging into Server||How do I connect to a Linux server?|
|00:30||3. 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?
|01:00||4. 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?
|01:50||5. 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?
|03:10||7. Downloading data||
How can I organize my file system for a new bioinformatics project?
How and where can data be downloaded?
|04:10||8. Assessing Read Quality and Trimming||
How can I describe the quality of my data?
How can I get rid of sequence data that doesn’t meet my quality standards?
|05:00||9. Sequence assembly||
How can the information in the sequencing reads be reduced?
What are the different methods for assembly?
|05:40||10. SNP phylogeny||How to generate a phylogenetic tree from SNP data?|
|06:55||11. Data Visualization||
How are phylogenetic trees viewed and compared?
How can I visualize several layers of data?
|08:05||12. Transmission?||In which cases is transmission likely?|
The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.