Short course

Analysing Microbial Genomic Data

Start date
Monday 1st - Friday 5th July 2024
5 days
Time commitment
35 hours
Genomics; Microbiology

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

This 5-day, hands-on 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 training will provide participants with the skills and knowledge required to plan, design, and analyse data from microbial genomics-based investigations.

With one of the largest communities of academic microbiologists in the world, the Institute of Microbiology and Infection is at the vanguard of innovative research into combatting threats to human health from infectious diseases and antimicrobial resistance. We do this by developing new approaches in three areas: diagnosis, treatment and prevention.  By bringing together a diverse community of internationally recognised researchers, we are developing strategies that range from novel antimicrobial surfaces, through hand-held DNA sequencers to novel drugs and vaccines.  At the heart of all these approaches is an unwavering dedication to ground-breaking, fundamental microbiology research – something that has been integral to the University of Birmingham since its foundation more than a century ago.

Dates of the course:

Monday 1st - Friday 5th July 2024. 

Course content:

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

Place availability:


How to apply:

Registration is open, you can register for the course using a debit/credit on the University's Online Shop.

The courses have minimum required attendance levels and the University reserves the right to cancel or postpone the course if the minimum required number of delegates has not been achieved for the course.

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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.


The course is not accredited. 

Course results:

Certificate of completion.

Learning outcomes:

  • Develop an understanding of what whole genome sequence data is, and how it is used in the context of microbial genomics
  • Competently use the command line to, for example, perform simple programming tasks such as string searches and automated loops using bash.
  • Carry out bioinformatic analysis of microbial genomic data including being able to retrieve raw sequence data from SRA; perform assembly, annotation, and SNP typing using raw sequence data; perform pangenome analysis of genome data sets; produce various types of phylogenetic tree
  • Understand the importance of microbial genomics in modern microbiology and make biologically meaningful interpretations from these data.
  • At the end of the course the attendee will be able to perform their own genomic analyses from raw data and understand which tools should be applied to specific questions in the future.