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Course Informatics Guide
Master cutting-edge genomics and bioinformatics approaches to advance viral diagnostics and investigation
The use of next-generation sequencing (NGS) has revolutionised the diagnosis and management of viral infections. Currently, clinical virology laboratories can perform whole genome sequencing and screening of hundreds of virus-infected samples within hours, enabling real-time genomics for diagnostics, transmission investigation, and infection control.
The course combines hands-on laboratory work with expert-led lectures focusing on cutting-edge NGS viral genome sequencing and analysis techniques. Participants will learn to prepare sequencing libraries using advanced methods like target enrichment and long-read technologies. The course offers practical training in bioinformatics, including the Linux/UNIX command line. It covers key aspects such as data quality control, reference mapping, de novo assembly of viral genomes, and phylogenetic analysis. Real-world case studies will highlight NGS’s practical applications and challenges in clinical settings.
This course is designed for virology researchers at the PhD, postdoc, or senior levels who are interested in mastering NGS of viral genomes. It’s also aimed at clinical virology and research scientists planning to implement NGS in diagnostic laboratories, offering essential insights into the latest genomic techniques and their future applications.
The course is approved annually for CPD accreditation by the Royal College of Pathologists (46 credits in 2024)
After attending this course, you will be able to:
- Conduct the full NGS process, from sample processing to bioinformatics analysis of patient-derived viral samples.
- Prepare and optimise sequencing libraries to improve output efficiency.
- Apply Linux/UNIX command line tools in analysis pipelines for whole viral genome and pathogen identification.
- Critically evaluate the limitations and potential applications of NGS in clinical viral diagnostics.
- Use phylogenetic analysis to identify transmission patterns and inform intervention strategies.
The course will cover:
- Overview: high-throughput sequencing and viral sequencing approaches.
- Library preparation: techniques for metagenomics and target enrichment, including probe-based and PCR-based methods.
- Bioinformatics analyses: tools and pipelines to data quality control, viral genome assembly, consensus and variant calling, metagenomics, multiple sequence alignment, and phylogenetic inference.
- Case studies: tailored sequencing approaches and bioinformatics pipelines for specific scenarios.
- Validation and accreditation: ensuring the reliability and standardisation of viral whole genome sequencing in diagnostic services.
- Group project: apply course concepts to solve real-world challenges.
Please note: Bioinformatic training will include the use of Linux/Unix command-line. As such, a prerequisite for this course is the completion of a Linux introductory course – familiarity with Linux and the command line is recommended in order to get the most from this course. There are numerous online introductory tutorials to the Linux/Unix operating system and command line, including:
Course Organisers
- Nick Loman, Institute for Microbiology and Infection, University of Birmingham, UK
- Tamyo Mbisa, Antiviral Unit, UK Health Security Agency, UK
- Emma Thomson, University of Glasgow, UKMRC Centre for Virus Research, University of Glasgow, UK
- Sreenu Vattipally, MRC Centre for Virus Research, University of Glasgow, UK
Course Instructors
- Anna da Silva Filipe, UK Health Security Agency, UK
- Richard Orton, University of Glasgow, UK
- Sunando Roy, University College, London, UK
- Kathy Smollett, University of Glasgow, UK
- Sarah Buddle, University College, London, UK
- David Bibby, UK Health Security Agency, UK
- Lilly Tong, University of Glasgow, UK
- Patricia Dyal Bynoe, University College London, UK
- Dulcibela Boampong, UK Health Security Agency, UK
Wellcome Connecting Science Team
- Alice Matimba, Head of Training and Global Capacity
- Cassandra Soo, Laboratory Courses Manager
- Aaron Dean, Laboratory Technical Officer
- Christopher Adamson, Laboratory Operations Officer
- Martin Asltett, Informatics Manager
- Vaishnavi Vikas Gangadhar, Informatics Technical Officer
The course data are free to reuse and adapt with appropriate attribution. All course data in these repositories are licensed under the Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0).
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