Microbial Genomics course 2019

In week 2 we will use publically available genome and RNA data from the organism Zymoseptoria tritici and related fungi. Outline and instructions (to be made available at the start of week 2) can be found here: https://drive.google.com/drive/folders/1_iTtzbKqk7j5uzMeN1R_lFgPGuF6KURl?usp=sharing

Schedule

		Setup	Download files required for the lesson
Day 1	09:00	1. Introduction	What are the goals of this practical training? What data do we work on?
	09:10	2. Logging onto Cloud	How do I connect to an AWS instance?
	09:20	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?
	09:50	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?
	10:40	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?
	11:25	6. Redirection	How can I search within files? How can I combine existing commands to do new things?
	12:10	7. Writing Scripts	How can we automate a commonly used set of commands?
	12:50	8. Project Organization	How can I organize my file system for a new bioinformatics project? How can I document my work?
	13:20	9. Assessing Read Quality	How can I describe the quality of my data?
	14:10	10. Trimming and Filtering	How can I get rid of sequence data that doesn’t meet my quality standards?
	15:05	11. Variant Calling Workflow	How do I find sequence variants between my samples and a reference genome?
	16:05	Finish
Day 2	09:00	12. Automating a Variant Calling Workflow	How can I make my workflow more efficient and less error-prone?
	10:15	13. R for microbial genomics	How can I use R to manipulate and visualize microbial genomic data?
	17:00	Finish
Day 3	09:00	14. Introduction Day3	Where does the dataset come from? How to login Where are the files located
	09:50	15. Sequence assembly	How can the information in the sequencing reads be reduced? What are the different methods for assembly?
	10:50	16. Sequence Quality	What is the N50 ? What are the different methods for assembly?
	11:20	17. Inspecting sequence graphs	Can we find out which scaffolds or contigs are connected?
	12:20	Finish
Day 4	09:00	18. Annotation	How are proteins predicted from a DNA sequence?
	10:00	19. Pangenome analysis	How to determine a pangenome from a collection of isolate genome sequences?
	11:00	20. Phylogenetic trees from the core genome	What is better, a gene presence absence tree or a tree from core genes/proteins Is there a specific clone associated with patient mortality
	12:00	21. Bacterial GWAS	Which genes are associated with patient mortality
	12:40	22. Wrapup Day 3 and 4	Do your findings match the published data?
	13:00	Finish

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

Microbial Genomics course 2019

Schedule week 1: Prokaryotic microbes (bacteria)

Schedule week 2: Eukaryotic microbes (fungi)

Data

Schedule