NGS Academy for the Africa CDC Pathogen Genomics Initiative

Advanced Training: Developing Workflows 2024

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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).

Intended audience:

Beginner - intermediate level bioinformaticians working with next-generation sequencing data for disease surveillance on the African continent

Purpose:

High-throughput laboratory machines generate large quantities of primary biological data. Processing these data to generate useful information involves several tools and setting up of complex bioinformatics environments across heterogeneous computing infrastructure. Bioinformatics workflow managers provide portability and reproducibility of analysis and optimization of available computing resources.

The Advanced Bioinformatics workflow workshop is aimed at introducing and deploying Nextflow, a tool that enables scalable and reproducible scientific workflows.

Pre-requisite:

  1. For the course, access to a high-performance computer will be organised by trainers
    2. Learning objective:
    1. To be able to implement a bioinformatics workflow using the best practices taught in previous iterations of the course

      2. The course will cover:

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      Logistics:

      1. Venue of course: KEMRI / WELLCOME TRUST Kilifi, Kenya
      2. Start date: 2024-05-20
      3. End date: 2024-05-24

      Themes Course materials Training partner Interactive Sessions with Instructor/s
    2. 1. Bacterial AMR
    3. 2. Metagenomics for diagnostics
    4. 3. Variant calling and phylogenetics
      		5.
        1. 1.1 ChatGPT
        2. 1.2 Julia
      • KEMRI-Wellcome Trust Research Programme,International Livestock Research Institute (ILRI),Malawi-Liverpool-Wellcome Trust
      • Dr George Githinji,John Juma, Phil Ashton

      Themes Course materials Training partner Interactive Sessions with Instructor/s
    5. 1. Bacterial AMR
    6. 2. Metagenomics for diagnostics
    7. 3. Variant calling and phylogenetics
      		8.
        Data sets
        1. 2.1 Project work
        2. - get main tools working in isolation (not in workflow)
        3. - to join the tools together into workflow
      • KEMRI-Wellcome Trust Research Programme, International Livestock Research Institute (ILRI),Malawi-Liverpool-Wellcome Trust
      • Dr George Githinji,John Juma, Phil Ashton

      Themes Course materials Training partner Interactive Sessions with Instructor/s
    8. 1. Bacterial AMR
    9. 2. Metagenomics for diagnostics
    10. 3. Variant calling and phylogenetics
      		11.
        1. 3.1 Project work
        2. -key tasks implemented in workflow
      • KEMRI-Wellcome Trust Research Programme, International Livestock Research Institute (ILRI),Malawi-Liverpool-Wellcome Trust
      • Dr George Githinji,John Juma, Phil Ashton

      Themes Course materials Training partner Interactive Sessions with Instructor/s
    11. 1. Bacterial AMR
    12. 2. Metagenomics for diagnostics
    13. 3. Variant calling and phylogenetics
      		14.
        1. 4.1 Project Work
        2. - workflow completed
        3. - write presentation
      • KEMRI-Wellcome Trust Research Programme, International Livestock Research Institute (ILRI),Malawi-Liverpool-Wellcome Trust
      • Dr George Githinji,John Juma, Phil Ashton

      Themes Course materials Training partner Interactive Sessions with Instructor/s
    14. 1. Bacterial AMR
    15. 2. Metagenomics for diagnostics
    16. 3. Variant calling and phylogenetics
      		17.
        2. 5.1 Project work
        3. - Presentations
      • KEMRI-Wellcome Trust Research Programme, International Livestock Research Institute (ILRI),Malawi-Liverpool-Wellcome Trust
      • Dr George Githinji,John Juma, Phil Ashton