University of the Free State | UFS | Universities | Next Generation Sequencing Unit


In the bid to respond to the upscaling need for capacity-building in bioinformatics and in genomic data analysis, a workshop entitled “Data and Bioinformatics Workshop 2023: From raw data to publication” was organized from 03 to 07 July 2023 by the University of the Free State – Next Generation Sequencing (UFS-NGS) Unit. Under the leadership of Prof. Martin Nyaga, Associate Professor at the University of the Free State, Head of the UFS-NGS Unit and Director of the WHO CC, the workshop brought together over 120 participants from across Africa, Europe and the USA. Participants came from more than fifteen research and university institutions in South Africa, and nearly a dozen collaborating institutions from elsewhere. 

The workshop was honoured by the participation of top UFS authorities, Prof. Joyce Tsoka-Gwegeni, Vice Dean, Faculty of the Health Sciences, Dr. Cornelius Hagenmeier, Director of the Office for International Affairs, Dr. Glen Taylor, Senior Director, Research and Internationalisation, and Prof. Jason Mwenda, the WHO/AFRO VPD Regional Coordinator. Eminent researchers with impressive achievements in the field of pathogen genomics research from South Africa, USA, Australia, Malawi and UK led the present workshop. As the unit’s name suggests, the topics covered were essentially related to pathogen genome mining, including 16S/ITS metagenomics data analysis aspects, Shotgun metagenomics data analysis, Whole genome data analysis aspects, Enteric and respiratory meta transcriptomics and metagenomics analysis aspects, Computational modelling for new chemical entity characterization. 

As a prelude to these topics, an introduction to “Command lines on Linux OS” were given, followed by some hands-on practice. The dry-lab training workshop has enabled participants to deal with (theoretically and with practical exercises) numerous bioinformatics terms, resources, and tools to be used in order to produce comprehensive, efficient and exploitable data that will benefit the community. It’s worth noting that arrangements were made by UFS and the organizers to ensure that participants could continue to apply the knowledge gained and make it sustainable, as they were given access to the HPC platform for over ten days after the end of the workshop. We believe that the participants are now sufficiently equipped and seasoned to undertake this scientific journey with us in the field of bioinformatics and sequencing data analysis. 

The UFS-NGS unit is a well-established and experienced provider of sequencing services for pathogens (bacteria, viruses, parasites, etc.) isolated from any matrix (human, animal, environment), as it promotes the “One Health” approach. It is also a WHO Collaborating Centre for Vaccine Preventable Diseases (VPD) Surveillance and Pathogen Genomics. We would like to thank the Distribution Platform in Omics (DIPLOMICS), the Bill and Melinda Gates Foundation (BMGF) and the World Health Organization (WHO/AFRO) for their ongoing support of the unit’s activities and their commitment to working alongside researchers to promote scientific research in Africa.