Blog / COG Train

14 Jul 2022

Bioinformatics for pathogen surveillance: Launching our third COG-Train online course

Launch of our third COG-Train online course “Making sense of genomic data: COVID-19 web-based bioinformatics”. Explore the tools for web-based SARS-CoV-2 sequencing analyses and learn techniques to prepare data and share genomic outputs.

Over the past decade, technological advances have enabled vastly improved genome sequencing capabilities and provided greater accessibility to sequencing for scientists in resource-constrained settings. This has resulted in the generation of huge volumes of sequencing data – thanks in no small part to the intensity of sequencing during the COVID-19 pandemic.

However, having mountains of data alone is not enough. For sequencing to have real world impact, you also need the sequencing pipelines (a method that uses software algorithms to process raw sequencing data to generate a list of annotated sequence variants) and bioinformatic tools to analyse genome sequences to understand their function and evolution.

Robust data storage and integration of metadata that can provide essential context are key to unlocking the potential for bioinformatic analyses to provide actionable information, and are arguably just as valuable as generating genome data. They can also enable existing datasets to be reused and amplified, allowing bioinformaticians to derive novel hypotheses from the available data.

Although many laboratories in Asia, Africa and Latin America have augmented their testing and sequencing capacity, bioinformatic analyses can still represent a critical barrier to the implementation of effective viral surveillance programmes. Indeed, discussions with over 50 of COG-Train’s global stakeholders, based in 26 different countries, identified bioinformatics capabilities as one of the major barriers to implementing pathogen surveillance. Aiming to serve the communities that formed part of our focus group, COG-Train have designed the third online course with this feedback in mind.

We are, therefore, delighted to announce the launch of Making sense of genomic data: COVID-19 web-based bioinformatics’.

By the end of this course learners will be able to:

  • Evaluate sequencing file formats
  • Perform data quality checks
  • Analyse SARS-CoV-2 sequencing data using web-based pipelines (Galaxy)
  • Identify and classify SARS-CoV-2 variants
  • Apply SARS-CoV-2 genomic analysis for epidemiological investigations

The course is designed for diagnostic and healthcare professionals, researchers, and anyone involved in the testing and analysis of disease samples. It will also be advantageous to researchers specialising in web-based bioinformatics, diagnostics, diseases, or pandemics. There are no formal prerequisites, though a basic knowledge of analysis tools using Galaxy or UNIX systems may be helpful. The completion of previous COG-Train courses is not a prerequisite for this course.

Who are the course educators?

The course educators and developers are experts in bioinformatics and viral genetics currently working on data analyses and SARS-CoV-2 bioinformatics:

  • Carolina Castañeda Garcia, PhD candidate at the International Laboratory for Human Genome Research, Mexico.
  • Claudine Nkera-Gutabara, PhD candidate in Human Genetics at the Sydney Brenner Institute for Molecular Bioscience, The University of Witwatersrand, South Africa.
  • Dr Tanya Golubchik, Senior Lecturer in Computational Microbiology, The Sydney Institute for Infectious Diseases, University of Sydney, Australia, and collaborating with the Big Data Institute at the University of Oxford, United Kingdom.
  • Tracey Calvert-Joshua, Bioinformatician, South African National Bioinformatics Institute, South Africa.
  • Varun Shamanna, Senior Bioinformatician, The Central Research Laboratory from the Kempegowda Institute of Medical Sciences, India.

What are the learning outcomes for this course?

  • Describe the SARS-CoV-2 viral genomic structure
  • Evaluate different sequencing analysis outputs
  • Apply a basic analytical web-based pipeline
  • Examine how variant calling contributes to epidemiological inferences

If you are involved in the testing and analysis of disease samples, are a diagnostic or healthcare professional, or if you are a researcher specialising in web-based bioinformatics, diagnostics, diseases, or pandemics, register your interest for this course now!

The course is due to be launched on 25th July 2022 and it will initially run until 26th September. If you are interested in participating, more information and registration details can be found here.



COVID-19 Genomics UK (COG-UK)

The COVID-19 Genomics UK (COG-UK) consortium works in partnership to harness the power of SARS-CoV-2 genomics in the fight against COVID-19.

Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative collaboration of NHS organisations, the four public health agencies of the UK, the Wellcome Sanger Institute and sixteen academic partners. A full list of collaborators can be found here.

The COVID-19 pandemic, caused by SARS-CoV-2, represents a major threat to health. The COG-UK consortium was formed in March 2020 to deliver SARS-CoV-2 genome sequencing and analysis to inform public health policy and to support the establishment of a national pathogen sequencing service, with sequence data now predominantly generated by the Wellcome Sanger Institute and the Public Health Agencies.

SARS-CoV-2 genome sequencing and analysis plays a key role in the COVID-19 public health response by enabling the identification, tracking and analysis of variants of concern, and by informing the design of vaccines and therapeutics. COG-UK works collaboratively to deliver world-class research on pathogen sequencing and analysis, maximise the value of genomic data by ensuring fair access and data linkage, and provide a training programme to enable equity in global sequencing.