Webinar: Bioinformatic analysis of pathogens for clinical and public health

Second part of the Introduction to Pathogen Genomics for Public Health webinar series

Webinar: Bioinformatic analysis of pathogens for clinical and public health

Part one: Tuesday 18 July 2023 13:00 - 16:00 (AEST)
Part two: Thursday 20 July 2023 13:00 - 15:30 (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 May, this is the second of a four-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:

  • To provide introductory understanding of bioinformatics processes for pathogen genomics
  • To understand the implication of data quality for downstream analyses
  • To understand 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 Jenny Draper, 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
  • Dr John-Sebastian Eden, Senior Research Fellow, University of Sydney and Westmead Institute for Medical Research
  • Mr Jacob May, Medical Scientist, South Australia Pathology
  • Dr Jake Lacey, Bioinformatics Section Support, Microbiological Diagnostic Unit Public Health Laboratory


Please register via this link.


Part one: Tuesday 18 July 2023 13:00 - 16:00 (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

Whole genome sequencing approach for antimicrobial resistance - Dr Jenny Draper

  • 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

Viral pathogens - Dr John-Sebastian Eden

  • Challenges/issues/considerations specific to viral pathogens and viral evolutions
  • Quasi species
  • Genetic differences of viral pathogens
Part two: Thursday 20 July 2023 13:00 - 15:30 (AEST)

Bioinformatic considerations for challenging organisms - Mr Jacob May

  • Considerations of fungal WGS
  • Correct identification of fungal species
  • Consideration of different growth stages
  • AMR and diploidy
  • Comparison of tools

Introduction to phylogenetics and cluster analysis - Dr Jake Lacey

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

Visualising techniques for cluster analysis - Dr Mitchell Sullivan

  • Visualisation techniques
  • Different cluster techniques, including phylogenetic branching, SNP distance (hierarchy clustering/pop punk), split KMER analysis, SNP profiles, cgMLST/MLST-like schemes, and defining SNP thresholds

Data reproducibility and version control of bioinformatic tools - Dr Joep de Ligt

  • Understanding challenges of classification of bacteria using WGS
  • Defining acceptance/rejection criteria for organism identification
  • Understanding taxonomic classification and continuous monitoring for updates to international standards
  • Validation, including when it has to be in-silico (no wetlab data to use)
  • AMR detection