Other pathogen surveillance courses

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The NGS Academy forms part of the Africa CDC Pathogen Genomics Initiative (PGI). This initiative is funded by the Bill & Melinda Gates Foundation. Our training initiatives are carried out in partnership with the African Society for Laboratory Medicine (ASLM).

Organisation

Course Title

Course Level

Context

Audience

Primary focus areas

Wellcome Connecting Science

Mathematical Models for Infectious Disease Dynamics

Beginner

Research/academia

Bioinformaticians based at health institutes and experimental biologists at research institutions

Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization, data management or a related topic

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
UK	Mathematical review (calculus, probability, etc.). Population dynamics. Deterministic and stochastic models. Modelling structured populations: age-structured, spatial and network models. (i) Applied programming with R. (ii) Statistical estimation of models. (iii) Computer-based simulations.	No	No	once a year or every two years	5 days	Face-to-face sessions, Virtual	No

Wellcome Connecting Science

Computational Molecular Evolution

Beginner

Research/academia

Bioinformaticians based at health institutes and experimental biologists at research institutions

Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization, data management or a related topic

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
UK	Data retrieval and assembly. Alignment techniques. Phylogeny reconstruction (including maximum likelihood and Bayesian methods). Hypothesis testing. Population genetics approaches. Protein and nucleotide sequence analysis, including NGS data (Please note however that the course focuses on NGS analyses for molecular evolution, we do not cover traditional NGS analyses e.g., QC, read mapping, variant calling, assembly etc.).	No	No	Once a year or every two years	5 days	Face-to-face sessions, Virtual	No

Wellcome Connecting Science

Systems Biology: From Large Datasets to Biological Insight

Beginner

Research/academia

Bioinformaticians based at health institutes and experimental biologists at research institutions

Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization, data management or a related topic

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
UK	Data reduction and data integration methods – including comparison of major approaches through lectures and practical exercises. Machine and deep learning – practical exercises on supervised machine learning, including classification and regression, and deep learning. Functional inference from omics data – approaches to extract signatures of cell state from -omics data including transcription factor activation and kinase activity states. Extraction of upstream signalling pathways from transcriptomics datasets. Network inference and signal propagation – network inference approaches from -omics data.	No	No	Once a year or every two years	5 days	Face-to-face sessions, Virtual	No

Wellcome Connecting Science

Working with Protozoan Parasite Database

Beginner

Research/academia

Bioinformaticians based at health institutes and experimental biologists at research institutions

Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization, data management or a related topic

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
UK	Visualisation of sequence features and next generation sequencing data using the Artemis genome browser and annotation tool. Genome browsing and comparative genomics (ACT and JBrowse/GBrowse). Formulating complex biological queries in computationally accessible form. Web-based resources including the GeneDB.org and VEuPathDB.org family of databases. Integrating functional genomics data (RNA-seq, ChIP-seq, ChIP-chip, microarrays, proteomics, etc) with genome sequence data. Theoretical aspects of genome re-sequencing. Querying genetic diversity on a genome-wide scale. Metabolic pathways and pathway and GO enrichment analysis. Working with next-generation sequence data (mapping, variant calling, RNA-Seq etc) using both command-line and web-based (Galaxy) methods. Introduction to community curation tools	No	No	Once a year or every two years	5 days	Face-to-face sessions, Virtual	No

Wellcome Connecting Science

RNA transcriptomics

Beginner

Research/academia

Bioinformaticians based at health institutes and experimental biologists at research institutions

Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization, data management or a related topic

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
UK	Overview of single molecule long read sequencing technologies. Full length total RNA sequencing. Full length cDNA sequencing. Small RNA sequencing. Single cell transcriptome data generation and analysis. Identification of post-transcriptional modifications in RNA (epi-transcriptomics). Functional assays for lncRNA biology. Integration of microRNA and mRNA data; functional analysis of microRNAs. Expression network and pathway integration and analysis	No	No	Once a year or every two years	5 days	Face-to-face sessions, Virtual	No

Wellcome Connecting Science

Fungal Pathogen Genomics

Beginner

Research/academia

Bioinformaticians based at health institutes and experimental biologists at research institutions

Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization, data management or a related topic

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
UK	Perform RNA-seq and SNP analysis and visualization via EuPathDB Galaxy workspace in FungiDB. Identify secondary metabolite clusters in MycoCosm. Find virulence genes and annotation in Ensembl. Access genetic interactions in CGD/SGD. Comparative genomics and browsers: GBrowse, JBrowse, ACT, Artemis, Ensembl. Use of Apollo annotation tools for fungal genomes. Web-based resources for fungal genomic data including: FungiDB, EnsemblFungi, PomBase, SGD/CGD, MycoCosm/JGI, etc.. Identification of orthologs, and orthology-based inference (using OrthoMCL, Compara, etc.). Next generation sequence analysis, including variant calling (EuPathDB Galaxy). RNA-Seq analysis and visualization. Developing advanced biologically relevant queries, using FungiDB ‘search strategies’. Best practices using ontologies to generate hypotheses and analyse data (ontology structure, evidence, available tools, slimming and enrichment, etc.).	No	No	Once a year or every two years	5 days	Face-to-face sessions, Virtual	No

Wellcome Connecting Science

Genomics and Clinical Virology

Beginner

Research/academia

Bioinformaticians based at health institutes and experimental biologists at research institutions

Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization, data management or a related topic

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
UK	Background to viral WGS approaches. Sample handling and preparation. Library preparation techniques. Target enrichment methods e.g. probe-based sequence capture or PCR-based. Viral metagenomics. Technique discrimination – the appropriate technique to use in different scenarios. Next generation and third generation sequencing platforms. Bioinformatics analysis including different viral genome assembly approaches. Data interpretation. Validation and accreditation of viral WGS diagnostic service, Case studies in outbreak investigation and infection control.	No	No	Once a year or every two years	5 days	Face-to-face sessions, Virtual	No

Wellcome Connecting Science

Genomics and Clinical Microbiology

Beginner

Research/academia

Bioinformaticians based at health institutes and experimental biologists at research institutions

Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization, data management or a related topic

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
UK	Data analysis, display and dissemination. Design, implementation, and interpretation of real-time PCR tests for pathogen detection. Molecular approaches to detect multiple pathogens. Whole genome sequencing (WGS). PCR and sequence-based isolate characterisation. Outbreak investigation and applications to public health. Bioinformatics and data interpretation. Data analysis, display and dissemination	No	No	Once a year or every two years	5 days	Face-to-face sessions, Virtual	No

Wellcome Connecting Science

Malaria Experimental Genetics

Beginner

Research/academia

Bioinformaticians based at health institutes and experimental biologists at research institutions

Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization, data management or a related topic

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
UK	CRISPR-Cas9 based approaches. Consideration of the relative merits of different conditional expression approaches. Mechanics of transfection in P. falciparum and P. knowlesi. Verification of gene targeting using multiple genotyping techniques. Drug-response assays of genome edited parasites. Application of next generation sequencing to transcriptional profiling and quantitating parasite growth. Flow cytometry-based phenotyping platforms.	No	No	Once a year or every two years	5 days	Face-to-face sessions, Virtual	No

Wellcome Connecting Science

Antimicrobial Resistance in Bacterial Pathogens

Beginner

Research/academia

Bioinformaticians based at health institutes and experimental biologists at research institutions

Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization, data management or a related topic

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
UK	Historical and epidemiological aspects of antimicrobial resistance (AMR). Clinical importance of AMR. Causes and biological mechanisms of resistance in Gram-positive and Gram-negative bacteria. Antimicrobial susceptibility testing (AST) methods, e.g. disc testing, automated systems, minimum inhibitory concentration (MIC), breakpoints and reporting. Molecular methods for detection of AMR. Internal quality control (QC) and external quality assurance (QA) for AST. AMR pathogens in Africa. AMR in veterinary medicine. Antibiotic policies and stewardship. AMR surveillance methods and study design. Tackling AMR using a One Health Approac. Introduction to genomic surveillance of AMR. Local AMR epidemiology – investigating transmission of clones and AMR. Analysis of resistance in genomes	No	No	Once a year or every two years	5 days	Face-to-face sessions, Virtual	No

Wellcome Connecting Science

Helminth Bioinformatics

Beginner

Research/academia

Bioinformaticians based at health institutes and experimental biologists at research institutions

Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization, data management or a related topic

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
UK	The WormBase ParaSite database. IGV/JBrowse genome browsers. Variant calling. Differential gene expression. Unix/Linux command-line. Introduction to R	No	No	Once a year or every two years	5 days	Face-to-face sessions, Virtual	No

Wellcome Connecting Science

Next Generation Sequencing Bioinformatics

Beginner

Research/academia

Bioinformaticians based at health institutes and experimental biologists at research institutions

Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization, data management or a related topic

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
UK	Introduction to NGS technologies. Introduction to the unix command line. NGS data formats and tools. Sequence alignment and QC. SNP/indel theory and practical. Structural variation theory and practical. RNA-seq analysis. ChiP-seq analysis. Sequencing data visualisation with the Integrated Genomics Viewer (IGV). Accessing public sequencing repositories. Genome assembly theory and practical. Participant projects and presentations	No	No	Once a year or every two years	5 days	Face-to-face sessions, Virtual	No

Wellcome Connecting Science (Makerere University)

Viral Genomics and Bioinformatics

Beginner

Research/academia

Bioinformaticians based at health institutes and experimental biologists at research institutions

Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization, data management or a related topic

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
Uganda	Introduction to Linux/Unix. NGS file formats. NGS data quality check and cleaning. Reference assembly. Assembly statistics and visualisation. Consensus and variant calling. De novo assembly. De novo contig consolidation and gap filling. Pathogen sequence detection using sequence classifiers. BLAST. Sequence submission. Multiple sequence alignment. Recombination detection. Introduction to phylogenetics methods. BASH scripting	No	No	Once a year or every two years	5 days	Face-to-face sessions, Virtual	No

Wellcome Connecting Science (KEMRI)

Molecular Approaches to Clinical Microbiology in Africa

Beginner

Research/academia

Bioinformaticians based at health institutes and experimental biologists at research institutions

Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization, data management or a related topic

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
UK	Fundamental molecular biology techniques including preparing, handling, and storing DNA. PCR, including real-time PCR, with an emphasis on, methods, applications and data interpretation. Determining sequence variation, its visualisation and interpretation, concentrating on conventional approaches. Bioinformatic analysis of molecular and genomic data, particularly the exploitation of web-based tools. An overview of future technologies, and their potential for application in clinical microbiology.	No	No	Once a year or every two years	5 days	Face-to-face sessions, Virtual	No

Wellcome Connecting Science

Genomics and Epidemiological Surveillance of Bacterial Pathogens

Beginner

Research/academia

Bioinformaticians based at health institutes and experimental biologists at research institutions

Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization, data management or a related topic

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
UK	Practical bioinformatics skills needed to manipulate raw sequence data (some of which will be generated on the course), including: mapping and de novo assemblies, SNP calling, annotation and analysis of genomic information. Sequence analysis and comparative genomics of next generation sequencing data using Artemis and ACT. Principles of phylogeny and construction of accurate phylogenies. Group exercises designed to teach everyday skills required to work in genomic surveillance. Practical exercises for using GPS to map cases of infectious disease and phenotypes (such as AMR) across the world.	No	No	Once a year or every two years	5 days	Face-to-face sessions, Virtual	No

Wellcome Sanger Institute

Bioinformatics training - JUNO/GPS

Beginner

Research/academia

Bioinformaticians based at health institutes and experimental biologists at research institutions

Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization, data management or a related topic

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
UK	Visualisation, Genomics, Phylogentcics, Clustering, MLST, serotyping, PathogenWatch, Microreact.	No	No	N/A	N/A	Virtual	No

MRIGlobal

COVID-19 Virtual Lab Training for Genomic Epidemiology

Intermediate

Research/academia

Experimental biologists at research institutions and laboratory technicians in public health labs

Epidemiology, Sample processing, DNA/RNA extraction, Library prep, Sequencing

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
USA	RNA extraction in BSC Clinical specimen (mock NP swab sample) Library Preparation in Sequencing Lab Pre-amplification area and Post-amplification area Reagent preparation at start of day Qubit Analyzer to check libraries for concentration and quality Load sequencer flow cells and reagent cartridge Sequencing run- Miseq Review of results after sequencing run Upload of data to Explify or Illumina software	Yes	Not yet	Regular intervals	5-7 days	Pre-recorded materials	Plan subtitles in French

Johns Hopkins University

JHU/NCDC Sequencing Workshop

Intermediate

Research/academia

Broad audience of laboratory scientists and bioinformaticians at health or research institutions

Epidemiology, Sample processing, DNA/RNA extraction, Library prep, Sequencing, Bioinformatics

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
USA	Module 1.Introduction to Pathogen Sequencing Module 2.Introduction to Genomic Epidemiology Module 3.Sequencing with the MinION: Laboratory Methods Module 4.Sequencing with the MinION: Loading and Interpretation Module 5.Introduction to Bioinformatics Module 6.Running the Assembly Pipeline (including Command Line Introduction) Module 7.Working with Sequence Data Module 8.Sequence Alignments and Building Trees Module 9.Interpreting Phylogenetic Trees	No	No	Other	Two 1-2 hour Zoom sessions per week for 4 weeks. Participants are expected to watch up to 1 hour of pre-recorded material between sessions, and to attempt laboratory methods or bioinformatic analysis as appropriate.	Pre-recorded materials	Yes - pre-recorded videos will have English and French subtitle options. All materials and slides will be available in English.

Dalhousie University

Canadian Bioinformatics Workshop: Infectious Disease Epidemiology Analysis

Intermediate

Research/academia

Graduates, postgraduates, staff bioinformaticians, laboratory technologists, medical microbiologists and PIs working with or about to embark on analysis of genomic and metagenomics data for epidemiological investigations.

Epidemiology, Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization, data management or a related topic

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
Canada	Understand next generation sequencing (NGS) platforms as applied to pathogen genomics and metagenomics sequencing - Analyze NGS data for pathogen surveillance and outbreak investigations - Analyze antimicrobial resistance genes - Detect emerging pathogens in metagenomics data - Perform phylogeographic analysis - Use different visualization tools for genomic epidemiology analysis	No	No	Presented at regular intervals	3-day workshop with lectures and hands-on tutorials usually in-person although digital during COVID.	Face-to-face sessions, Live, remote sessions	No

Chan Zuckerberg Biohub

Metagenomic Sequencing for Detection, Identification and Surveillance of Infectious Disease

Beginner

Research/academia

Experimental biologists at research institutions and in public health settings

Pathogen genomics for clinicians, Sample processing, DNA/RNA extraction, Library prep, Sequencing, Bioinformatics

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
USA	Sample collection; lab set up; enrichment strategies (amplicon based)	No	No	Other	5-day workshop when remote. We would extend into a two-week workshop with hands-on wet lab work..	Face-to-face sessions, Live, remote sessions	No

IsraelX

Essentials of Genomics and Biomedical Informatics

Advanced

Research/academia

Life science researchers; Health science research; Biomedical science researchers

Epidemiology, Sequencing, Bioinformatics, Data analysis, data visualization, data management or a related topic

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
Israel	https://www.edx.org/course/essentials-of-genomics-and-biomedical-informatics	Yes, weekly quizzes and practical assignments	Yes, there is verified certificate for $49	Presented at regular intervals	2-3 hours per week for 12 weeks	Pre-recorded materials	Video transcript: English, Hebrew, Arabic

University of Colorado

Genetic Epidemiology Foundations

Intermediate

Public health

Life science researchers; Health science research; Biomedical science researchers

Epidemiology, Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization, data management or a related topic, Biostatistics

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
USA	https://www.coursera.org/learn/genetic-epidemiology	Weekly or Modular practice exercises and quizzes	Yes, course offers 'Certificate of Completion' after successful completion	Constantly available	Approximately 17 hours to complete entire course. Start instantly and learn at your own schedule.	Pre-recorded materials	Course is presented in English with Subtitles in English

University of Virginia

Bacterial Bioinformatics

Intermediate

Research/academia

Experimental biologists at research institutions; trainers in bioinformatics settings; health personnel; students in life science field/programmes.

Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization, data management or a related topic

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
USA	https://www.coursera.org/learn/informatics	Weekly practice exercise and quizzes	Yes, course offers 'Certificate of Completion' after successful completion	Presented at regular intervals	1 - 3 hours per week, or approximately 14 hours to complete	Pre-recorded materials	Presented in English with Subtitles including French, Portuguese (European), Russian, English, Spanish

Technical University of Denmark

Whole genome sequencing of bacterial genomes - tools and applications

Beginner

Research/academia

Experimental biologists at research institutions; trainers in bioinformatics settings; health personnel; students in life science field/programmes.

Pathogen genomics for clinicians, Sequencing, Bioinformatics, Data analysis, data visualization, data management or a related topic

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
Denmark	https://www.coursera.org/learn/wgs-bacteria	Weekly or Modular quizzes	Yes, course offers 'Certificate of Completion'	Other	Approximately 7 hours to complete the modules.	Pre-recorded materials	Subtitles are provided in the following languages: Arabic, French, Portuguese (European), Italian, Vietnamese, German, Russian, English, Spanish

Johns Hopkins University

Metagenomics applied to surveillance of pathogens and antimicrobial resistance

Beginner

Public health

Experimental biologists at research institutions

Epidemiology, Pathogen genomics for clinicians, Sample processing, DNA/RNA extraction, Library prep, Sequencing, Bioinformatics

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
USA	https://www.coursera.org/learn/metagenomics/home/info	Short quizzes which are (MCQs - multiple choices questions)	Yes - The course offers 'Certificate of Completion'	Presented at regular intervals	1 - 3 hours per week - approximately 15 hours to complete entire course	Pre-recorded materials	Yes, course is available in English; Subtitles available in French, Portuguese (European), Russian, English, Spanish

Universidad de los Andes

Applied bioinformatics, molecular epidemiology, and the SARS-CoV-2 pandemic

Intermediate

Research/Academia

Bioinformaticians based at health institutes, and experimental biologists at research institutions

Epidemiology, Pathogen genomics for clinicians, Sample processing, DNA/RNA extraction, Bioinformatics, Data analysis, data visualization, data management or a related topic

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
Colombia	https://www.ebi.ac.uk/training/events/cabana-workshop-applied-bioinformatics-molecular-epidemiology-and-sars-cov-2-pandemic/	Final exam	No	Other	4 days	Live remote sessions	No

Chan Zuckerberg Initiative

Foundations of Genomic Epidemiology

Beginner

Public health

Applied epidemiologists, public health microbiologists, lab directors working on bringing genomic sequencing into their lab.

Data analysis, data visualization, data management or a related topic

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
USA	Inferring genetic divergence trees, molecular clocks and time trees, phylogeography, consensus genome QC, genomic epi sampling design, Pango nomenclature, pathogen-specific genomic epi.	No	No	Presented at regular intervals	1 Hour seminar	Pre-recorded	No

Centers for Disease Control and Prevention/ OAMD

AMD Academy Bioinformatics course

Intermediate

Public health

State, local, and territorial public health laboratories in the United States.

Sequencing, Bioinformatics, Data analysis, data visualization, data management or a related topic

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
USA	Introduction to Bioinformatics Introduction to Bacterial Genomics Intro to Linux Environment Bioinformatics resources for public health Getting things done in Linux Quality control of NGS Data Genome Assembly Sequence alignment and searching Pathogen Characterization and Annotation Genetic inference Data Visualization Communication of NGS data	Yes	No; the course does offer CEU via APHL.	Other	Typically 5-day in person workshop. Other offerings were in place during COVID-19.	Face-to-face sessions, Live, remote sessions, Pre-recorded materials	No

Centers for Disease Control and Prevention

Molecular Epidemiology for Epidemiologists

Beginner

Public health

Epidemiologists working in US state and local health departments.

Epidemiology, Data analysis, data visualization, data management or a related topic

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
USA	Microbial evolution Next-gen sequencing technology Genome assembly Phylogenetic trees hqSNP and MLST Epidemiologic inference from sequence data Phenotypic inference (antimicrobial resistance) Outbreak investigation Network analysis (contact tracing) Diagnostics Challenges in IT and data integration	Not at present, planned for online	Not at present, planned for online	Present at regular intervals	Two-day workshop with lectures and hands-on exercises.	Face-to-face sessions, Live, remote sessions, Pre-recorded materials	No

NGS Academy for the Africa Pathogen Genomics Initiative

Next Generation Sequencing Bioinformatics Training Course

Intermediate

Research/academia

Postdoctoral scientists, senior PhD students, junior faculty members or clinicians/healthcare professionals based in Africa who are actively engaged in or soon to commence research involving next generation sequencing data analysis.

Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization, data management or a related topic, Biostatistics

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
Cape Town South Africa	The programme will cover the following topics: Intro to Unix/Linux & running workflows, Introduction to NGS Technologies, NGS data pre-processing and QC, Alignment to reference sequences, Variant calling and annotation, ChIP-Seq â€¢ RNA-Seq and Genome assembly	Includes multiple tests and assignments	Course certificate will be offered	Present at regular intervals	The course will run for 8 weeks on Tuesdays and Thursdays (4 hours per session) from the 13th of April until the 10th of June 2021	Face-to-face sessions, Live, remote sessions, Pre-recorded materials	No

Institut Pasteur de Tunis

Introduction to NGS Technologies and their applications

Beginner

Research/academia

Mainly experimental biologists at research institutions

Sequencing

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
Tunisia	- Human Genome Project - Evolution of Sequencing Technologies - Databases and resources to retrieve relevant Omics information - Applications of NGS	No	Not alone, but as part of a H3ABioNet course	Present at regular intervals	2 hours long	Pre-recorded materials	No

University of Glasglow

Glasglow Bioinformatics Summerschool

Beginner

Research/academia

Experimental biologists at research institutions

Bioinformatics, Data analysis, data visualization, data management in the context of public health, pathogen genomics and epidemiology

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
Glasglow, UK	Basics of Linux Introduction to R Introduction to next-generation sequencing Data visualization SNP analysis Transcriptomics: bulk RNA-Seq and single-cell RNA-Seq Databases Data processing	No	No, just internal for PhD students	Presented at regular intervals	5 day workshop	Live, remote sessions, Face to Face	Now all material availble through zoom, where an automatic transcript is available.

University of Pennsylvania

VEuPathDB workshop

Beginner

Research/academia

Experimental biologists

Bioinformatics, Data analysis, data visualization, data management or a related topic as would be applicable in the context of public health, pathogen genomics and epidemiology

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
Philadelphia, USA	See this years course, material and recordings: https://veupathdb.org/veupathdb/app/static-content/workshops.html#veupath2021	No	No	Other	5-day workshop with lectures and hands on exercises. Students work both individually and in groups to achieve exercise objectives.	Live, remote sessions, Face to Face	No

Wellcome connecting science

Working with pathogen genomes

Beginner

Research/academia

Bioinformaticians based at health institute

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
Cambridge UK	Introduction to pathogen genomics Introduction to Artemis Using the Linux operating system for bioinformatics Comparative genomics using the Artemis Comparison Tool (ACT) Mapping Illumina sequence data against a reference genome Genome-wide phylogenetic analysis using SNPs Genome assembly Genome annotation Transcriptome analysis using RNA-seq data Two extended practical sessions applying the above topics	No	No	Presented at regular intervals	5 day course	Live, Remote sessions, Face to Face, Pre-recorded materials	No

Monash University

SARS-CoV-2 Sequencing and bioinformatics

Beginner

Research/academia

Researchers and public health officials interested in viral genomics and bioinformatics.

Library prep, Sequencing, Bioinformatics, Data analysis, data visualization, data management or a related topic as applicable to public health, pathogen and genomics

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
Malaysia	Under development	No	Yes	Other	5 day workshop	Face to Face	English is the medium of instruction

Wellcome connecting science

Working with Pathogen Genomes, Asia

Beginner

Research/academia

Researchers working in the field of infectious diseases in Asia.

Pathogen genomics for clinicians, Sample processing, DNA/RNA extraction

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
Bangkok Thailand	Click here	exercises were used to consolidate participants learning	Yes	Other	5-day workshop	Live, remote sessions, Face to Face	A handbook was provided, but presentations were given live

University of Ibadan

Introduction to Bioinformatics for Bacterial Genomics

Beginner

Public health

Postgraduate students

Bioinformatics, Data analysis, data visualization, data management or a related topic as would be applicable in the context of public health, pathogen genomics and epidemiology

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
Ibadan, Nigeria	Introduction to Bioinformatics Theoretical Concepts and Approaches in Bioinformatics Hands-on Bioinformatics Analyses (GUI and Web-based Tools) Introduction to the Unix Command Line	No	No	Presented at regular intervals	10 day workshop	Live, remote sessions, Pre-recorded materials	Course offered in English only

University of Ibadan

Sustainable development in bioinformatics to support public health

Beginner

Public health

Hospital Laboratory Scientists and Field epidemiologists interested in integrating bioinformatics within their health institute and field.

Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization, data management or a related topic

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
Nigeria	1. Next-Generation Sequencing technologies 2. The use of online platforms and user-friendly workflows to conduct bioinformatic analyses (genome assembly, speciation, SNP phylogeny, AMR gene prediction), 3. How to visualize and interpret the results from bioinformatic analyses	No	No	Other	A one or two-week course every month for three months	Pre-recorded materials	No

Makerere University

Applied Microbial Genomics

Intermediate

Research/academia

Bioinformaticians based at health institutes, experimental biologists at research institutions

Epidemiology, Pathogen genomics for clinicians, Sequencing, Bioinformatics, Data analysis, data visualization, data management or a related topic

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
Uganda	Bioinformatics tools in clinical microbiology	Yes	Yes	Constantly available	Hour long seminar	Live, remote sessions	English

Wellcome connecting science

Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R

Beginner

Research/academia

Bioinformaticians based at health institutes and experimental biologists at research institutions

Bioinformatics, Data analysis, data visualization, data management or a related topic (as would be applicable in the context of public health, pathogen genomics and epidemiology

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
Cambridge, UK	What is Linux? Why Linux for biologists? The Linux file system and navigating around it via the command line Manipulation and searching of data files using the command line to access useful biological data The basics of writing Bash scripts and its use for process automation Guidelines and recommendations for best practice preparation of data files under Linux for exporting to other environments (use of R for further analysis and visualisation) Exercising on biological data using different case scenarios	Yes, multiple choice. Accredited	Certification of completion	Presented at regular intervals	2 weeks at your own pace	Online but some support	Yes, English subtitles

Wellcome connecting science

Bacterial Genomes: Antimicrobial Resistance in Bacterial Pathogens

Beginner

Research/academia

Bioinformaticians based at health institutes and experimental biologists at research institutions

Pathogen genomics for clinicians, Bioinformatics

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
Cambridge, UK	Significance and challenges of AMR and the need for control of antibiotic use Mechanisms of antibiotic action, resistance and evolution Antimicrobial susceptibility testing Molecular detection and characterisation of AMR resistance genes Recent developments in genomic technology for tackling AMR	Yes, multiple choice questions	Certification of completion	Presented at regular intervals	3 weeks at your own pace	Online	English

Wellcome connecting science

Bacterial Genomes I: From DNA to Protein Function Using Bioinformatics

Beginner

Research/academia

Bioinformaticians based at health institutes and experimental biologists at research institutions

Pathogen genomics for clinicians, Bioinformatics Data analysis, data visualization, data management or a related topic as would be applicable in the context of public health, pathogen genomics and epidemiology

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
Cambridge, UK	Bioinformatics tools, DNA and protein sequences Retrieving DNA and protein sequences from repositories Databases for protein annotation • Inferring function from sequence	Yes	Royal College of Pathologists. 10 Credits	Constantly available	2 weeks at your own pace	Online	English

Wellcome connecting science

Bacterial Genomes II: Accessing and Analysing Microbial Genome Data Using Artemis

Beginner

Research/academia

Bioinformaticians based at health institutes and experimental biologists at research institutions

Pathogen genomics for clinicians, Bioinformatics Data analysis, Data visualization, data management or a related topic as would be applicable in the context of public health, pathogen genomics and epidemiology

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
Cambridge, UK	Multi-FASTA files Reference and draft bacterial genomes Introduction to Artemis, an open source genome browser Genome annotation Genomic regions defined by GC (guanine-cytosine) content Accessing and downloading whole genome sequences Pathogenicity islands Peer-reviewed project: Ecological niche adaptation between two Mycobacterium species Pseudogenes in Mycobacterium species	Yes, multiple choice questions	Royal College of Pathologists. 15 Credits	Constantly available	3 weeks at your own pace	Online	English

Wellcome connecting science

Bacterial Genomes III: Comparative Genomics using Artemis Comparison Tool (ACT)

Beginner

Research/academia

Bioinformaticians based at health institutes and experimental biologists at research institutions

Pathogen genomics for clinicians, Bioinformatics, Data analysis, Data visualization, data management or a related topic as would be applicable in the context of public health, pathogen genomics and epidemiology

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
Cambridge, UK	Introduction to comparative genomics, Introduction to ACT, Analyse available data, Generate your own comparison files, Make your own comparisons in ACT, Identify pseudogenes in Mycobacterium leprae using ACT, Peer review project: Comparative genomics on two clinically relevant plasmids from Shigella	Yes, multiple choice questions	Royal College of Pathologists. 15 Credits	Constantly available	3 weeks at your own pace	Online	English

Wellcome connecting science

Train the Trainer: Design Genomics and Bioinformatics Training

Beginner

Research/academia

Bioinformaticians based at health institutes and experimental biologists at research institutions

Bioinformatics, Data analysis, data visualization, data management or a related topic as would be applicable in the context of public health, pathogen genomics and epidemiology

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
Cambridge, UK	Adult learning and teaching principles and approaches for small or large groups. Social learning through knowledge sharing; role of teacher/trainer in a learner centred environment. Iterative process of learning design and development applied to genomics training. Common educational methods to teach and assess bioinformatics and laboratory methods required for genomics. Peer review project: design training in genomics, evaluate, reflect and improve.	Yes	No	Presented at regular intervals	3 weeks	Online	Course offered in English only

Thermo Fisher Scientific

Bioinformatics for molecular biologists

Beginner

Research/academia

Biologist with no prior experience in bioinformatics

Data analysis, data visualization, data management or a related topic (as would be applicable in the context of public health, pathogen genomics and epidemiology)

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live or Online	With subtitles
Johannesburg, South Africa	Course is broken up in 3 modules namely Linux Python/Pearl MySQL The aim is to provide introductory training in order to get participants comfortable to script and start using linux based software	No	yes, Training Certificate from Thermo Fisher	Course is scheduled as needed, with standing courses as well through the year	5 day hands on instructor led training either face to face or virtual	In person or Online	None

Fleming Fund Regional Grant SEQAFRICA

SARS-CoV-2 whole genome sequencing

Intermediate

Research/academia

Users with some experience/knowledge of whole genome sequencing (WGS) and WGS data.

Epidemiology

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
Copenhagen, Denmark	Agenda available on course website: click here	No	No	Constantly available	The course was originally an online course over 4 half-days consisting of live and pre-recorded lectures and hands-on exercises.	Face-to-face sessions and pre-recorded materials	No

Fogarty International Center, National Institutes of Health

FIC/JHU Workshop for Implementation of Genomic Epidemiology

Beginner

Research/academia

For laboratorians already doing techniques such as RT-PCR/qRT-PCR that were interested in sequencing their own samples, analyze them using phylogenetics, and be able to interpret the results epidemiologically.

Epidemiology, Sample Processing, Library prep Bioinformatics

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
Usually UAE, as it is easy for most participants to travel to and get visas.	Pre-workshop Software Installation Sessions: Day 1: Introduction to Genomics Technologies and Oxford Nanopore Sequencing Day 2: Library Preparation, Sequencing, and Consensus Generation Day 3: Phylogenetics Day 4: Phylogenetics (Continued) Day 5: Wrap Up	no		On the basis of funding availability.	5 day workshop.	Face-to-face sessions & Remote	Subtitles in a variety of languages are available for pre-recorded materials. Interpreters have been used for live sessions.

Fogarty International Center, National Institutes of Health

FIC/JHU Genomic Epidemiology for Public Health Laboratories

Intermediate

Research/academia

For public health laboratorians already doing techniques such as RT-PCR/qRT-PCR that were interested in sequencing their own samples, analyze them using phylogenetics, and be able to interpret the results epidemiologically

Pathogen genomics for clinicians, Library prep, Sequencing, Bioinformatics, Biostatistics

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
Usually UAE, as it is easy for most participants to travel to and get visas.	Pre-workshop Software Installation Session Session 1: Genomic Epidemiology - Introduction and Laboratory Concepts Session 2: Processing and Visualizing Sequence Data Session 3: Phylogenetics Session 4: Phylogenetics (Continued) and Phylodynamics Session 5: Wrap Up	no		On the basis of funding availability.	5 day workshop.	Face-to-face sessions & Remote	Subtitles in a variety of languages are available for pre-recorded materials. Interpreters have been used for live sessions.

Fogarty International Center, National Institutes of Health

FIC/JHU Advanced Genomic Epidemiology

Advanced

Research/academia

For laboratorians and bioinformaticians with experience analyzing pathogen sequence data using phylogenetics based on maximum likelihood methods, and able to interpret the results epidemiologically, that want to learn more about phylodynamic and phylogeographic modeling.

Epidemiology,Sample processing DNA/RNA extraction, Library prep & sequencing

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
Usually UAE, as it is easy for most participants to travel to and get visas.	Pre-workshop Software Installation Session Session 1: Review of Laboratory and Phylogenetic Methods Session 2: Advanced Laboratory Design - Sampling Strategies and Sample preparation Session 3: Applied Informatics Session 4: Phylodynamics - Evolutionary and Temporal Patterns Session 5: Phylogeography - Spatiotemporal dynamics	no	no	On the basis of funding availability.	6 day workshop.	Face-to-face sessions & Remote	Subtitles in a variety of languages are available for pre-recorded materials. Interpreters have been used for live sessions.

Fogarty International Center, National Institutes of Health

FIC/JHU Applied Bioinformatics for Genomic Epidemiology

Advanced

Research/academia

For researchers with experience in sequencing techniques that want to process and analyze pathogen genetic data using bioinformatic approaches.

Epidemiology, Bioinformatics

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
Usually UAE, as it is easy for most participants to travel to and get visas.	Pre-workshop Software Installation Session Session 1: Workshop Introductions, Command-Line, and Bash Scripting Session 2: Regular Expressions, Working with Sequence Aligners / Databases / Classifiers Session 3: Practical Use for Oxford Nanopore Sequencing Applications Session 4: Working with Source Code, Package Managers, and Distributed Computing Session 5: Data Visualization	No. But questions are asked throughout the workshop to gauge the participant's assimilation of concepts	no	On the basis of funding availability.	5 day workshop.	Face-to-face sessions & Remote	Yes, all materials are available in English. Teachers speak English, Arabic, French, and Portuguese.

Public Health Institute Of Malawi

Clinical Bioinformatics for Healthcare

Beginner

Public Health

Trainers in Bioinformatics settings.

Bioinformatics

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
	Pre-workshop Software Installation Session Session 1: Intro to sequence data & QC Session 2: Genome assembly Session 3: Genome annotation Session 4: Bacteria subtyping Session 5: AMR detection Session 6: Phylogenetic analysis Session 7: Transmission analysis	No	Certificate by Wellcome Connecting Science	Presented at regular intervals	3-day workshop but it will extended to a week-long course next year.	Remote Live sessions	no

Wellcome Connecting Science/SAGESA

AMR Bioinformatics

Beginner

Public Health

This workshop was open to SAGESA network members based in Africa who were actively engaged in, or soon to commence, research, clinical practice, provision of clinical services, or policy development related to AMR in bacteria.

Epidemiology, Bioinformatics

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
	Pre-workshop Software Installation Session Session 1: Intro to sequence data & QC Session 2: Genome assembly Session 3: Genome annotation Session 4: Bacteria subtyping Session 5: AMR detection Session 6: Phylogenetic analysis Session 7: Transmission analysis	No	Certificate by Wellcome Connecting Science	Presented at regular intervals	3-day workshop but it will extended to a week-long course next year.	Remote Live sessions	no

Centre for Genomic Pathogen Surveillance, University of Oxford and Wellcome Connecting Science

How to Design and Deliver Pathogen Genomics Training for Health and Research Professionals

Intermediate

Public Health

Applicants from research, healthcare and training professionals who are involved in any aspect of genomics or data science, and who are interested in building their capabilities to effectively share their knowledge and skills with others focused on pathogen genomic analysis, application and interpretation in management of infectious disease. This includes clinical, biomedical, and public health scientists, epidemiologists, bioinformaticians.

Epidemiology,Pathogen Genomics for clinicians, Sample processing, Library prep, Sequencing,Bioinformatics, Biostatistics, Data Analysis,Data Visualization,data management

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
Wellcome Genome Campus, UK	Pre-workshop Software Installation Session Session 1: Genomics and data science Session 2: Training design	No	The course is approved for CPD accreditation by the Royal College of Pathologists (26 credits)	Presented at regular intervals	The course include self-paced online pre-course work followed by 3.5 days in-person sessions, consisting of lectures, hands-on exercises, genomic analysis demonstrations and group projects	On campus	no

Wellcome Connecting Science

Viral Genomics and Bioinformatics Asia 2022

Advanced

Research/Academia

PhD, Postdoc researchers, anyone needing to analyse viral sequencing data

Bioinformatics, Data Analysis,Data Visualization,data management

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
	Pre-workshop Software Installation Session Session 1: Genomics and data science Session 2: Training design	No	Yes, attendance certificate	It is part of the WCS courses program that alternates year by year	5 day course	Live remote sessions	yes, by Zoom automatically and on Youtube after

CDGN/APG

CDGN/APG Wet-lab processes for pathogen whole genome sequencing webinar

Beginner

Public Health

Registrars and consultants in medical microbiology and infectious diseases; scientists in public health and clinical microbiology;

Sample processing DNA/RNA,Library Prep, Sequencing

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
	Session 1: Implementation, validation, quality control and regulation	No	No	Yearly	2x 3hr session	Live remote sessions & pre-recorded	No

Theiagen Genomics

SARS-CoV-2 genomic epidemiology using the TheiaCoV workflow series and Terra bioinformatics platform

Intermediate

Public Health

Public health scientists without a bioinformatics background

Epidemiology,Pathogen Genomics for clinicians,Bioinformatics, Data Analysis, Data Visualisation

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
As requested by trainees	Session 1: Building Phylogenetic Trees for SARS-CoV-2 Session 2: Basics of interpreting phylogenies Session 3: More in-depth visualization and interpretation of SARS-CoV-2 phylogenies	No	Not currently	As requested	Taught seminars with hands-on data analysis tutorials; presented at the frequency requested (short online workshops over a number of weeks, or in-person intensive course)	Face to Face, Live remote sessions & pre-recorded	No

Theiagen Genomics

SARS-CoV-2 genomic epidemiology using the TheiaCoV workflow series and Terra bioinformatics platform

Intermediate

Public Health

Public health scientists without a bioinformatics background

Epidemiology,Pathogen Genomics for clinicians,Bioinformatics, Data Analysis, Data Visualisation

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
As requested for trainees	Session 1: Building Phylogenetic Trees for SARS-CoV-2 Session 2: Basics of interpreting phylogenies Session 3: More in-depth visualization and interpretation of SARS-CoV-2 phylogenies	No	Not currently	As requested	Taught seminars with hands-on data analysis tutorials; presented at the frequency requested (short online workshops over a number of weeks, or in-person intensive course)	Face to Face, Live remote sessions & pre-recorded	No

Theiagen Genomics

Influenza characterization and epidemiology using the TheiaCoV workflow series and Terra bioinformatics platform

Intermediate

Public Health

Public health scientists without a bioinformatics background

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
As requested for trainees	Session 1: Flu Genomics and Characterization Session 2: Flu Genomics Characterization on Terra Session 3: Introduction to Phylogenetics Session 4: Flu Phylogenetic analysis using Terra	No	Not currently	As requested	Training seminars and hands-on data analysis workshops, presented in any format as requested, e.g. an in-person multiday intensive course, or weekly short online sessions		Yes, translation of course materials and interpretation of live or pre-recorded presentation is available for any language upon request

Theiagen Genomics

Bacterial genome characterization using Theiagen workflows

Intermediate

Public Health

Public health scientists without a bioinformatics background

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
As requested for trainees	Session 1: Introduction to Terra, Data Upload and the TheiaProk Workflow Session 2: Bacterial Genome Assembly and Quality Control Session 3: Bacterial genome characterization Session 4: Course Review	No	Not currently	As requested	Training seminars and hands-on data analysis workshops, presented in any format as requested, e.g. an in-person multiday intensive course, or weekly short online sessions		Yes, translation of course materials and interpretation of live or pre-recorded presentation is available for any language upon request

Theiagen Genomics

Genomic characterization and epidemiology of food-borne infections using Theiagen workflows

Beginner

Public Health

Public health scientists without a bioinformatics background

Epidemiology

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
	Session 1: Introduction to Terra and the TheiaProk Workflow for Bacterial Genome Characterization Session 2: Bacterial Genome Assembly and Quality Control Session 3: Characterization of foodborne pathogens Session 4: Building Phylogenetic Trees for Foodborne Outbreaks Session 5: Interpreting Phylogenetic Trees Session 5: Course overview	No	Not currently		Training seminars and hands-on data analysis workshops, presented in any format as requested, e.g. an in-person multiday intensive course, or weekly short online sessions		Yes, translation of course materials and interpretation of live or pre-recorded presentation is available for any language upon request

Theiagen Genomics

Genomic characterization and epidemiology of healthcare-associated infections using Theiagen workflows

Intermediate

Public Health

Public health scientists without a bioinformatics background

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
	Session 1: Bacterial Genome Assembly, QC and Characterization Session 2: Antimicrobial Resistance and Mobile Genetic Elements Session 3: Building Phylogenetic Trees for Analysis of HAIs Session 4: Interpreting Phylogenetic Trees	No	Not currently		Training seminars and hands-on data analysis workshops, presented in any format as requested, e.g. an in-person multiday intensive course, or weekly short online sessions	Hybrid or any other method requested for trainees	Yes, translation of course materials and interpretation of live or pre-recorded presentation is available for any language upon request

Theiagen Genomics

Docker for Public Health Bioinformatics

Beginner

Public Health

Bioinformaticians based at health institutes

Bioinformatics, Systems administration

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
as required for trainees	Session 1: Introduction to Docker and Containerization Session 2: Container Repositories and Writing Dockerfiles Session 3: Developing custom docker files and docker images Session 4: The StaPH-B Docker-Builds Repository	No	Not currently		Training seminars and hands-on data analysis workshops, presented in any format as requested, e.g. an in-person multiday intensive course, or weekly short online sessions	Face to Face, Live, pre-recorded materials	Yes, translation of course materials and interpretation of live or pre-recorded presentation is available for any language upon request

Theiagen Genomics

Introduction to Workflow Management with WDL

Intermediate

Public Health

Bioinformaticians based at health institutes

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
---	Session 1: Introduction to the WDL Workflow Manager Session 2: A Deeper Dive into WDL Session 3: The Dockstore Repository and WDL workflow Access through Terra Session 4: Course Review	No	No	other	Training seminars and hands-on data analysis workshops, presented in any format as requested, e.g. an in-person multiday intensive course, or weekly short online sessions	Hybrid or any other method requested for trainees	Yes, translation of course materials and interpretation of live or pre-recorded presentation is available for any language upon request

Theiagen Genomics

Introduction to Workflow Management with Nextflow

Intermediate

Public Health

Bioinformaticians based at health institutes

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
---	Session 1: Getting Started with Nextflow Session 2: The nf-core Project Session 3: Use of Nextflow Tower Session 4: Administration of the Nextflow Tower Instance Session 5: Course Review	No	No	other	Training seminars and hands-on data analysis workshops, presented in any format as requested, e.g. an in-person multiday intensive course, or weekly short online sessions	Hybrid or any other method requested for trainees	Yes, translation of course materials and interpretation of live or pre-recorded presentation is available for any language upon request

University of Melbourne

Microbial Genomics: DNA Sequencing Basics (Melbourne MicroCert)

Beginner

Public Health

Infectious Disease Professionals, Infectious Disease Physicians, Medical Registrars, Medical Microbiologists, Epidemiologists, Public Health Physicians, Laboratory Scientists, Other Health Professionals

Pathogen genomics for clinicians, Sample processing DNA/RNA extraction, Library prep, Sequencing, Bioinformatics

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
---	Session 1: Explore the fundamental science of DNA sequencing Session 2: Discover best-practice DNA sequencing approaches Session 3: Understand quality control approaches and lab workflows Session 4: Analyse pathogen genomic DNA sequence data	Quiz: Application of DNA sequencing technologies and approaches to diverse scenarios (40%) Independent analysis of pathogen genomic DNA sequence data (60%)	Micro-Credential	Yearly	4 weeks (40 hours), 9 hours online lectures 5 hours self-directed learning 6 hours discussion groups 4 hours instructor led practical activity 16 hours assessment tasks	Live remote sessions and pre-recorded materials	Most of the material is written content

University of Melbourne

Microbial Genomics: Bioinformatic Analysis Basics (Melbourne MicroCert)

Beginner

Public Health

Pathogen genomics for clinicians, Sample processing DNA/RNA extraction, Library prep, Sequencing, Bioinformatics

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
---	Session 1: Explore the fundamental science of DNA sequencing Session 2: Discover best-practice DNA sequencing approaches Session 3: Understand quality control approaches and lab workflows Session 4: Analyse pathogen genomic DNA sequence data	Quiz: Application of DNA sequencing technologies and approaches to diverse scenarios (40%) Independent analysis of pathogen genomic DNA sequence data (60%)	Micro-Credential	Yearly	4 weeks (40 hours), 9 hours online lectures 5 hours self-directed learning 6 hours discussion groups 4 hours instructor led practical activity 16 hours assessment tasks	Live remote sessions and pre-recorded materials	Most of the material is written content

Peter Doherty Institute

SARS-CoV-2 Illumina Sequencing

Beginner

Public Health

Lab scientists

Epidemiology, Sample processing DNA/RNA extraction, Library prep, Sequencing, Bioinformatics, Data analysis, data visualisation, data management

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
Locally or in-country	Session 1: Introduction to NGS, ONT Sequencing of SARS-CoV-2 Session 2: Analysis of SARS-CoV-2 Run Results, Session 3: ONT Run Metrics Session 4: WGS of Bacteria Session 5: ONT for Influenza Sequencing Session 6: WGS of Bacteria Session 7: Tiled Amplicon Sequencing of SARS-CoV-2 Session 8: Analysis of Bacterial WGS ONT Run Results	No, we do ask that trainees send us results of their first few runs so we can help evaluate them.	No	Available by request	Often 1-2 weeks with a mixture of lectures, hands-on lab work and discussions	Face to Face	No, but we can explore this option.

Peter Doherty Institute

SARS-CoV-2 ONT Sequencing

Beginner

Public Health

Lab scientists

Epidemiology, Sample processing DNA/RNA extraction, Library prep, Sequencing, Bioinformatics, Data analysis, data visualisation, data management

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
Locally or in-country	Session 1: ONT Sequencing Session 2: Bacterial WGS Session 3: ONT MinKNOW EPI2ME Run Metrics	No	No	-	1-2 weeks. Mixture of lectures, hands-on work and discussions	Face to Face	No, but we can explore this option.

Peter Doherty Institute

Bacterial Illumina Sequencing

Beginner

Public Health

Lab scientists

Epidemiology, Sample processing DNA/RNA extraction, Library prep, Sequencing, Bioinformatics, Data analysis, Data visualisation, Data management

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
Locally or in-country	Session 1: Illumina Sequencing Session 2: Bacterial WGS Session 3: Illumina Data Management Session 4: Galaxy Session 5: Introduction to Microbial Sequencing	No	No	-	1-2 weeks. Mixture of lectures, hands-on work and discussions	Face to Face	No, but we can explore this option.

Peter Doherty Institute

Bacterial ONT Sequencing

Beginner

Public Health

Lab scientists

Epidemiology, Sample processing DNA/RNA extraction, Library prep, Sequencing, Bioinformatics, Data analysis, data visualisation, data management

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
Locally or in-country	Session 1: ONT Sequencing Session 2: Bacterial WGS Session 3: ONT MinKNOW EPI2ME Run Metrics	No	No	-	1-2 weeks. Mixture of lectures, hands-on work and discussions	Face to Face	No, but we can explore this option.

Peter Doherty Institute

PulseNet Asia Pacific Illumina Sequencing

Beginner

Public Health

Wet Lab scientists

Epidemiology, Sample processing DNA/RNA extraction, Library prep, Sequencing, Bioinformatics, Data analysis, data visualisation, data management

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
Locally (Melbourne) and in-country	Session 1: Bioinformatics from a Wet Lab Perspective Session 2: Bioinformatics in Public Health Session 3: Introduction to NCBI & Data Sharing Session 4: Introduction to Illumina Session 5: ONT Sequencing Session 6: Illumina Sequencing Session 7: Terra.bio (Theiagen)	No	Yes we have initial certification and yearly proficiency testing	Presented at regular intervals	1-2 weeks. Mixture of lectures, hands-on lab work and dicusssions.	Face to Face, Live remote sessions	No, but we can explore this option.

Peter Doherty Institute

Genomics for Clinicians

Intermediate

Public Health

Clinicians, ID Physicians etc.

Pathogen Genomics for clinicians, Sample processing DNA/RNA extraction, Library prep, Sequencing, Bioinformatics

Location	Sub-topics	Formal assessment	Accredited	Available	Duration	Live/Online	With subtitles
Locally or in-country	Session 1: DNA Extraction Session 2: Illumina Sequencing Session 3: ONT Sequencing Session 4: Basic Data Interpretations Session 5: PHL Workflows Session 6: Manual Handling vs Automation	No	No, the course is a component of a larger training program for ID clinicians.	Presented at regular intervals	1 week. Mixture of lectures, hands-on training and discussions.	Face to Face	No, but we can explore this option.

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Primary focus areas