Advanced Training: Developing Workflows 2022


Click here for the training survey
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).

Course overview:

High-throughput laboratory machines generate large quantities of raw biological data. Processing the data to generate useful information involves using several tools and sometimes setting up complex bioinformatics analysis environments across heterogeneous computing devices. Bioinformatics workflows and workflow managers allow reproducibility and portability of analysis plans and optimization of available computing resources. The Advanced Training: Developing Workflows workshop was aimed at introducing, deploying Nextflow, a too which enables scalable and reproducible scientific workflows.

Intended audience:

Beginner - Intermediate level Bioinformaticians working with next-generation sequencing data in East-Africa.

Pre-requisite:
  1. For the course, participants do not need a high-performance computer since the trainers will provide access to KEMRI's cluster
  2. The course will cover:

    ...
    ...
    ...
    ...
    ...

    Logistics:


    1. Venue of course: KEMRI / WELLCOME TRUST Kilifi, Kenya
    2. Start date:2022-04-25
    3. End date:2022-04-29
    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

    Course schedule and Materials:

    Day 1 Training Videos

    Session Course materials Training partner Interactive Sessions with Instructor/s
    9:00am - 10:00am
    • Introduction to the Course
      1. 1. Draw Scientific Journey (Includes your current needs for intermediate/advanced training)
      2. 1.1 Get setup working on HPC
    • Malawi-Liverpool-Wellcome Trust
    • KEMRI
    • Dr Philip Ashton
    • Dr George Githinji
    10:30am - 1:00pm
    • Malawi-Liverpool-Wellcome Trust
    • KEMRI
    • Dr Philip Ashton
    • Dr George Githinji
    2:00pm - 4:00pm
    • Malawi-Liverpool-Wellcome Trust
    • KEMRI
    • Dr Philip Ashton
    • Dr George Githinji

    Day 2 Training Videos

    Session Course materials Training partner Interactive Sessions with Instructor/s
    9:00am - 10:00am
    • 1. Recap from yesterday
    • 1.1 Introduction to docker mounts and volumes
    • 1.2 Working with volumes and persisting data
    • 1.3 Introduction to singularity
    • Malawi-Liverpool-Wellcome Trust
    • KEMRI
    • Dr Philip Ashton
    • Dr George Githinji
    10:30am - 1:00pm
    • Malawi-Liverpool-Wellcome Trust
    • KEMRI
    • Dr Philip Ashton
    • Dr George Githinji

    2:00pm - 3:00pm
    • KEMRI
    • Dr George Githinji

    Day 3 Training Videos

    Session Course materials Training partner Interactive Sessions with Instructor/s
    9:00am - 1:00pm
    • Malawi-Liverpool-Wellcome Trust
    • KEMRI
    • Dr Philip Ashton, Belson Kutambe
    • Dr George Githinji

    2:00pm - 4:00pm
    • 2. Running snakemake.
    • 2.1 Run snakemake with conda
    • 2.2 Running snakemake on HPC
    • 2.3 Practical: Snakemake
    • Malawi-Liverpool-Wellcome Trust
    • KEMRI
    • Dr Philip Ashton, Belson
    • Dr George Githinji

    Day 4 Training Videos

    Session Course materials Training partner Interactive Sessions with Instructor/s
    9:00am - 10:00am
    • 1. Running Snakemate cont...
    • ILRI
    • KEMRI
    • Malawi-Liverpool-Wellcome Trust
    • John Juma
    • Dr George Githinji
    • Belson Kutambe
    10:30am - 1:00pm
    • 2. Sharing pipelines
    • Malawi-Liverpool-Wellcome Trust
    • KEMRI
    • ILRI
    • Dr Philip Ashton, Belson Kutambe
    • John Juma
    2:00pm - 4:00pm
    • 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