TRIUMPH Microbial Genomics course

COINCIDE edition.

Prokaryotic microbes - Assembly, annotation, pangenome analysis and GWAS

This practical is part of the Microbial Genomics practical course of Utrecht University adapted for the JPIAMR TRIuMPH project.

  1. Working with genome assemblies, QC and annotation of genomes
  2. Pangenome analysis, genomic phylogenetic trees and GWAS
  3. Sequence type, resistance genes, mutations and plasmids

Data

We will make use of E. coli genomes sequencing using Nanopore sequencing. The genomes have different resistance patterns and in this course we will identify which gene(s) are responsible for the resistance.

In the lessons you will learn how to assemble genomes, how to check for problems in assemblies, how to annotate genomes, how to work with annotations, how to determine the pan genome and the core genome and you will associate gene presence/absence with phenotypes using contingency testing (“GWAS”). Additionally you will learn how to make phylogenetic trees, determine MLST type and detected resistance genes and mutations of the strains.

Schedule

Setup Download files required for the lesson
Day 1 08:00 1. Welcome
08:15 2. Introduction How to speak the languange of the commandline
Where does the dataset come from?
How to login
Where are the files located
10:15 3. Sequence Read Quality Lecture How does sequencing work
Where do the errors come from
10:40 4. Sequence assembly How can the information in the sequencing reads be reduced?
What are the different methods for assembly?
11:50 Finish
Day 2 08:00 5. Introduction day 2
08:10 6. Sequence Assembly Lecture How can the information in the sequencing reads be reduced?
What are the different methods for assembly?
How can we assess the quality of an assembly?
08:40 7. Sequence Quality What is the N50 ?
What are single copy chromosomal marker genes ?
09:40 8. Self Study: Inspecting sequence graphs Can we find out which scaffolds or contigs are connected?
09:40 9. MLST How can we detect the MLST type
10:20 10. Resistance genes How can we detect the resistance genes and point mutations
11:10 Finish
Day 3 08:00 11. Introduction day 3 - work on day 2 exercises by yourself
09:00 12. Plasmid typing and classification How can we detect which contig is a plasmid and which is from the chromosome
10:00 13. Annotation How are proteins predicted from a DNA sequence?
11:00 14. Visualizing genomic regions using Clinker How does the genetic region of your resistance gene look like
12:00 Finish
Day 4 08:00 15. Introduction day 4
08:10 16. Pangenome analysis How to determine a pangenome from a collection of isolate genome sequences?
09:10 17. Phylogenetic trees from the core genome and visualization Is there a specific clone associated with resistance
10:50 18. Self Study: Bacterial GWAS Lecture Can we associate the presence of genes with phenotypes
What is population structure correction
How do we deal with false positives?
10:50 19. Self Study: Bacterial GWAS Which genes are associated with resistance
10:50 20. Wrapup Do your findings match the resistance genes detected?
11:10 Finish

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