Australia and New Zealand
Australian Government Department of Health
Implementation plan for the National Microbial Genomics Framework 2021–2022
National Microbial Genomics Framework 2019-2022
Public Health Laboratory Network|
New Zealand ESR genomics and next generation sequencing
CDGN authorship guidance
International
Centers for Disease Control and Prevention (Genomics and precision health)
Public Health England (Genomics)
Wellcome Sanger Institute
COVID-19 Genomic Epidemiology Toolkit
WHO Sequencing strategies and implementation to detect SARS-CoV-2 variants
Member laboratories
NSW
Institute of Clinical Pathology and Medical Research (ICPMR), Westmead Hospital
SEALS (South Eastern Area Laboratory Services) Pathology
QLD
Pathology Queensland
Queensland Health Forensics and Scientific Services (QHFSS)
Sullivan Nicolaides Pathology
VIC
Microbiological Diagnostic Unit Public Health Laboratory (MDU), The University of Melbourne
Victorian Infectious Diseases Reference Laboratory (VIDRL)
Useful bioinformatics links
AUSTRAKKA is an integrated genomics platform for rapid sharing and analysis of genomic data across all states and territories in Australia. The AUSTRAKKA platform is being used to conduct real-time analysis of integrated pathogen genomic data for public health across Australia.
GitHub is a development platform that brings teams of software developers together to write code and manage projects. Bioinformaticians use the GithHub repository to share code, collaborate effectively with fellow peers and store source code for popular /highly respected bioinformatic tools.
The International Nucleotide Sequence Database Collaboration (INSDC) captures and preserves a spectrum of data raw reads, through alignments and assemblies and provide access to comprehensive public domain nucleotide sequence and associated metadata. The long-standing collaboration operates between the DNA Data Bank of Japan DDBJ, the European Nucleotide Archive (ENA) at the European Molecular Biology Laboratory's European Bioinformatics Institute EMBL-EBI and GenBank at National Center for Biotechnology Information NCBI.
PHA4GE is a global coalition that is actively working to establish consensus standards; document and share best practices; improve the availability of critical bioinformatic tools and resources; and advocate for greater openness, interoperability, accessibility and reproducibility in public health microbial bioinformatics.
FDA GenomeTrakr is the first distributed network of labs to utilize whole genome sequencing for pathogen identification. Data curation and bioinformatic analyses and support are provided by the National Center for Biotechnology Information (NCBI) at the National Institutes of Health.