NGS Academy for the Africa CDC Pathogen Genomics Initiative

Advanced Training: Developing Workflows 2023 (Advanced)

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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).

Advanced Stream

Click Introductory stream to access the introductory stream training materials

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 was 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 was organised by trainers

    2. The course will cover:

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    Logistics:

    1. Venue of course: KEMRI / WELLCOME TRUST Kilifi, Kenya
    2. Start date: 2023-03-27
    3. End date: 2023-03-31
    Course curriculum:
    1. Day 1 HPC and introduction to containers
    2. Day 2 Introduction to git and file organisation
    3. Day 3 Introduction to snakemake
    4. Day 4 Advanced workflows (Nextflow, CWL)
    5. Day 5 Practical application

    Session Course materials Training partner Interactive Sessions with Instructor/s
    9:00am-10:30am
    • NGS Academy/UCT
    • Tony Li
    • Kirsty Lee Garson
    10:30am-1:00pm
    • 1.2 Advanced python
      1. 1.3 Writing your own classes
      2. 1.3.1 Lecture & Practical
    • Malawi-Liverpool-Welcome Trust
    • Dr Philip Ashton
    1:00pm-5:00pm
    • 1.3 Advanced Python cont..
      1. 1.3.2 Writing your own classes
    • Malawi-Liverpool-Welcome Trust
    • Dr Philip Ashton

    Session Course materials Training partner Interactive Sessions with Instructor/s
    9:00am - 10:30am
    • Day 2 slides & files
    • 2.0 Advanced python
    • 2.1 Using common bioinformatics modules (Bio python )
    • 2.2 Lecture and practical
    • 2.3 Best practices
    • Malawi-Liverpool-Welcome Trust
    • Dr Philip Ashton
    10:30am - 1:00pm
    • 2.2 Scientific talk
    • KEMRI
    • Dr Charles Sande

    2:00pm - 5:00pm
    • 2.3 Nextflow.
    • 2.4 Introduction to Nextflow.
    • 2.5 Channels
    • 2.5 Processes
    • ILRI
    • John Juma

    Session Course materials Training partner Interactive Sessions with Instructor/s
    9:00am - 10:30pm
    • Day 3 slides & files
    • 3. Nextflow
    • 3.1 Simple RNA-seq1 pipeline
    • 3.2 nf-core pipelines
    • 3.3 nf-core tools
    • ILRI
    • John Juma

    2:00pm - 5:00pm
    • 3.6.0 Advanced containerisation.
    • 3.6.1 Singularity
    • 3.6.2 Creating your singularity container
    • 3.6.3 Working with singularity and the HPC
    • KEMRI
    • Dr George Githingi

    Session Course materials Training partner Interactive Sessions with Instructor/s
    9:00am - 10:30am
    • Malawi-Liverpool Welcome Trust
    • Dr Philip Ashton
    10:30am - 2:00pm
    • 4.2. Practical project work

      Select a Bioinformatics paper from the collection below, and design a workflow to replicate it. What will you use - conda, docker, snakemake? What tools will you need? Are they available via those channels?
    • Malawi-Liverpool-Wellcome Trust
    • KEMRI
    • ILRI
    • Dr Philip Ashton, Belson Kutambe
    • John Juma
    2:00pm - 4:00pm
      1. 4.3 Practical project work cont...
    • ILRI
    • KEMRI
    • John Juma
    • Dr George Githinji

    Session Course materials Training partner Interactive Sessions with Instructor/s
    9:00am - 1:00pm
    • Practical project on implementing your own workflow
    • KEMRI
    • Malawi-Liverpool-Wellcome Trust
    • Dr George Githinji
    • Dr Philip Ashton