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
Data
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 | |
| 00:00 | 1. Introduction |
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? |
| 02:35 | 6. Redirection |
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? |
| 08:30 | Finish |
The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.