Molecular Epidemiology of Infectious Diseases - computer practical

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

  1. Tuesday, 9.30 - 12.15: Intro to data and the command line, downloading data
  2. Wednesday, 9.30 - 12.15: Trimming, SNP-based phylogeny, assembly
  3. Thursday, 9.30 - 12.15: Annotation, pangenome analysis, visualizations, conclusions

Data

This computer practical uses data from this publication We are using this collaborative document.

Schedule

Setup Download files required for the lesson
Day 1 00:00 1. Introduction What are the goals of this practical training?
What data do we work on?
00:10 2. Logging into Server How do I connect to a Linux server?
00:20 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?
00:50 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?
01:40 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?
02:25 6. Redirection How can I search within files?
How can I combine existing commands to do new things?
03:00 7. Downloading data How can I organize my file system for a new bioinformatics project?
How and where can data be downloaded?
04:00 Finish
Day 2 00:00 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?
00:50 9. SNP phylogeny How to generate a phylogenetic tree from SNP data?
02:35 10. Sequence assembly How can the information in the sequencing reads be reduced?
What are the different methods for assembly?
03:50 Finish
Day 3 00:00 11. Annotation How are proteins predicted from a DNA sequence?
01:00 12. Pangenome analysis How to determine a pangenome from a collection of isolate genome sequences?
02:00 13. Data Visualization How are phylogenetic trees viewed and compared?
How can I visualize several layers of data?
02:40 14. Transmission? In which cases is transmission likely?
03:05 Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.