Analysing microbial genomic data

The generation and analysis of genome sequencing data is rapidly becoming a commonplace requirement in microbiology research laboratories and clinical and public health microbiology laboratories. However, many microbiologists shy away from incorporating genomics into their research or lab practices, feeling that extensive skills in bioinformatics are required to analyse such data.

This 5-day course is designed to provide microbiologists with the ability to perform high-level analysis of microbial genomic data sets, regardless of background knowledge or ability. A mixture of seminars from world leading researchers, discussion fora and guided hands-on training will provide participants with the skills and knowledge required to plan, design, and analyse data from microbial genomics based investigations, be they fundamental research or public health epidemiological investigations.

Course Overview

  • Genome data formats, retrieving sequence data from repositories, and QC
  • De novo genome assemblies and annotation
  • Mapping and SNP calling
  • Pangenome analysis
  • Phylogenetics
  • Interpreting your data

Learning outcomes

  • Competently use ubuntu operating systems and usage of command line
  • Perform assembly, annotation, mapping, comparative genomics and phylogenetics on large genome data sets
  • Automate tasks on large data sets using bash commands
  • Making biological interpretations from genomic data

Who is the course for?

The course is designed for anyone with an interest in analysing microbial genomic data. No prior knowledge of bioinformatics is required, though participants will be asked to work through an online tutorial on using the command line prior to the course. All participants will be proficient in data analysis by the end of the course. We encourage PhD students, post-doctoral researchers, research fellows and early-career PIs, and clinical and public health microbiologists to attend