NGS Academy for the Africa CDC Pathogen Genomics Initiative

Advanced Training: Developing Workflows 2023 (Introductory)

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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).

Introductory Stream

Click Advanced stream to access the advanced 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-12:00pm
    • 1.2 Introduction to Conda and Conda environments
      1. 1.3 Miniconda Installation
      2. 1.4 Use of mamba
      3. 1.5 Conda environments
      4. 1.6 Different ways of specifying (cmd line, yaml file)
      5. 1.7 Ways of saving/exporting/sharing
      6. 1.8 Practical
      7. 1.9 Lecture
    • KEMRI
    • Dr George Githinji
    1:00pm-5:00pm
    • 1.9.0 Introduction to Containers
      1. 1.9.1 Introduction to docker
      2. 1.9.2 Finding and rolling out containers
      3. 1.9.3 Run docker
      4. 1.9.4 Build a docker container
      5. 1.9.5 Modifying a docker container
      6. 1.9.6 Sharing a docker container via docker hub
      7. 1.9.7 Theory session on singularity, similarities and differences with docker
      8. 1.9.8 S materials (CLIMB)
    • KEMRI
    • Dr George Githinji

    Session Course materials Training partner Interactive Sessions with Instructor/s
    9:00am - 10:30am
    • KEMRI
    • Dr George Githinji
    10:30am - 1:00pm
    • 2.2 Scientific talk
    • KEMRI
    • Dr Charles Sande

    2:00pm - 5:00pm
    • 2.3 File organisation.
    • KEMRI
    • Dr George Githinji

    Session Course materials Training partner Interactive Sessions with Instructor/s
    9:00am - 1:00pm
    • Day 3 slides & files
    • 3. Introduction to Snakemake
    • 3.1 Scripting
    • 3.2 Basic concerpts
    • 3.3 Running a basic pipeline
    • 3.4 Configurations
    • 3.5 Combined lecture & practicals (Snakemake)
    • Malawi-Liverpool-Wellcome Trust
    • Dr Philip Ashton, Belson Kutambe

    2:00pm - 5:00pm
    • 3.6.0 Running snakemake.
    • 3.6.1 Run snakemake with conda
    • 3.6.2 Running snakemake on HPC
    • 3.6.3 Practical: Snakemake
    • Malawi-Liverpool-Wellcome Trust
    • Dr Philip Ashton, Belson

    Session Course materials Training partner Interactive Sessions with Instructor/s
    9:00am - 10:30am
    • Day 4 slides & files
    • 4.0 Advanced workflows (Nextflow and CWL)
    • 4.1 Compare and contrast with snakemake
    • ILRI
    • John Juma
    10:30am - 1:00pm
    • 4.2. Nextflow practical
    • Malawi-Liverpool-Wellcome Trust
    • KEMRI
    • ILRI
    • Dr Philip Ashton, Belson Kutambe
    • John Juma
    2:00pm - 4:00pm
      1. 4.3 Practical project work
    • 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
    • John Juma