Webinar: Bioinformatic analysis of pathogens for clinical and public health

Want to gain expertise in whole genome sequencing? Join this free webinar series.

Webinar: Bioinformatic analysis of pathogens for clinical and public health

Part one: Tuesday 20 September 2022 13:00 - 16:15 (AEST)

Part two: Wednesday 28 September 2022 13:00 - 16:45 (AEST)


Are you a clinical scientist, medical microbiologist or infectious diseases physician wanting to gain an understanding of the application of bioinformatics for pathogen genomics in public health?

Following on from the wet-lab webinar held in July, this is the second of a three-part webinar series co-hosted by the Communicable Diseases Genomics Network (CDGN) and the Australian Pathogen Genomics Program.

Learning outcomes

Key learning outcomes of the second webinar in the Introduction to Pathogen Genomics for Public Health Webinar Series include:

  • Overview of bioinformatics processes for pathogen genomics
  • Understanding the implication of data quality for downstream analyses
  • Knowledge of the limitations associated with different bioinformatics processes

Webinar facilitators

  • Dr Lex Leong, Pathogen Genomics Lead, South Australia Pathology
  • Dr Joep de Ligt, Senior Science Lead Bioinformatics & Genomics, Institute of Environmental Science and Research
  • Dr Kristy Horan, Bioinformatics Section Leader, Microbiological Diagnostic Unit Public Health Laboratory
  • Dr Elena Martinez, Bioinformatician, Institute of Clinical Pathology and Medical Research
  • Dr Stanley Pang, Senior Bioinformatician, PathWest
  • Dr Mitchell Sullivan, Bioinformatics Analyst, Forensic and Scientific Services, Queensland Health
  • Ms Patricia Wolf, Bioinformatician, Forensic and Scientific Services, Queensland Health
  • Ms Cara Minney-Smith, Acting Medicial Scientist in Charge, Pathwest


Registrations have now closed.


Part one: Tuesday 20 September 2022 13:00 - 16:15 (AEST)

Assessment of sequence quality and filtering - Dr Lex Leong

  • Recognise the differences between raw sequence outputs
  • Understand the differences between long and short read sequence data
  • Be able to explain the QC metrics required to pass a run/sample.
  • Understand the trimming process (when or if trimming required)

Methods of whole genome sequencing assembly - Dr Stanley Pang

  • Understand the differences between assembly methods
  • Recognise the differences between tools used in de novo assembly, mapping and hybrid

Species identification and subtyping - Dr Kristy Horan

  • Understand the differences between kmer, alignment, and profile-based identification
  • Understand the concepts of MLST, cgMLST, and SNP distances, and their different levels of resolution
  • Awareness that genomic and traditional serotyping/laboratory methods may be discordant

Analysis and reporting example: Salmonella example - Ms Cara Minney-Smith

  • Understand the process required to determine serovars in Salmonella
  • Recall differences obtained through different serotyping tools
  • Interpreting clusters of Salmonella outbreaks with the help of epi data.
  • Use of Nullabor pipeline for salmonella

Part two: Wednesday 28 September 2022 13:00 - 16:45 (AEST)

Whole genome sequencing approach for antimicrobial resistance - Dr Elena Martinez

  • Understanding different methods & tools
  • Comparing both gene detection vs mutational resistance detection
  • Database & nomenclature challenges
  • Be mindful of the challenges present in in silico AMR determination

Introduction to phylogenetics and cluster analysis - Ms Patricia Wolf

  • Recognise the common phylogenetic models used and other variables
  • Understand that different organisms have different cluster thresholds

Overview of shotgun metagenomic sequencing of clinical specimens - Dr Mitchell Sullivan

  • Understand different types of metagenomics analysis and what each can tell us, eg. Species ID, AMR, typing
  • Understand different tools for analysis, including tools for targeted panels vs shotgun metagenomics
  • Understand the importance of controls and how to use them for interpreting results