Microbial Genomics course 2022: Glossary

Key Points

Welcome
Introduction	Sequencing S. pneumoniae patient isolates to determine assocations of bacterial genes with disease severity
Sequence Read Quality Lecture	Determining sequence quality of reads
Morning break	coffee or tea
Sequence assembly	Assembly is a process which aligns and merges fragments from a longer DNA sequence in order to reconstruct the original sequence. k-mers are short fragments of DNA of length k
Sequence Assembly Lecture	Assembly is a process which aligns and merges fragments from a longer DNA sequence in order to reconstruct the original sequence. k-mers are short fragments of DNA of length k Quality can be assessed using N50 but also using other methods
Lunch break	Lunch break
Sequence Quality	Quality of a genome assembly can be assessed by looking at some basic statistics on the assembly, but also by using an external reference
Inspecting sequence graphs	A genome assembly is fragmented because of repeats in the genome. The assembly graph display possible connections between contigs.
Afternoon break	coffee or tea
Introduction day 2	Discussing issues from day 1 and day 2
Annotation	Genome annotation includes prediction of protein-coding genes, as well as other functional genome units It often starts by identifying open reading frames Predicted sequences are further analysed with BLAST Larger DNA sequences or genomes require automated prediction and annotation
Morning break	coffee or tea
Bacterial GWAS Lecture	GWAS is the association of genes, snps, kmers with phenotypes observed Population structure is needed to correct for linkage disequilibrium Multiple testing correction is needed to deal with false positives
Pangenome analysis	The microbial pangenome is the union of genes in genomes of interest. The microbial core genome is the intersection of genes shared by genomes of interest. Roary is a pipeline to determine genes of the pangenome.
Lunch break	Lunch
Phylogenetic trees from the core genome	A tree can be generated from a combined set of proteins for better resolution
Bacterial GWAS	Contigency testing for gene presence absence to associate a genotype with a phenotype, similar to GWAS in clinical genetics is possible with bacterial genomes
Wrapup	Phage-Derived Protein Induces Increased Platelet Activation and Is Associated with Mortality in Patients with Invasive Pneumococcal Disease

Glossary

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