Target audience: 25 PhD/Postdoc researchers who are actively working on AMR/Microbiology and require training in basic bioinformatics
Bacteria and Parasites
When: Week of 15 December 2019 (TBC)
Suggested topics:
-Introduction to Bioinformatics
o What is bioinformatics
o Applicability to microbiology genomics research
- The different sequencing platforms available
o What is the difference and what level of discrimination they offer
Single gene sequencing vs WGS
o   Difference sequencing platforms: long vs. short reads
- How to design your project and ask the research question
- Know the pathogen you are researching – what to look for
- Basic of primer design
- Using BLAST
- GenBank
- Basic Sequence alignments
o Identifying Single nucleotide polymorphisms (SNPs), mutations and gene variants
- Assessing the quality of your sequences – length and quality
o Finding promotor regions
o Start and end codons of the target gene
- Basics of Multi-locus sequence typing (MLST)
- Typing methodologies for epidemiological investigations
o Single gene, MLST, cgMLST & WGS
- Next generation sequencing: importance and applicability
- Platforms available for pathogen genomics
- Identifying plasmids & virulence factors from WGS data
Offer 1:1 consultation to discuss individual needs/projects