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University of Cape Town’s Computational Biology Group

NGS Data Analysis and Galaxy Workshop

Instructors: Dave Clements, Gerrit Botha

21-25 October 2013

The course is hosted by the University of Cape Town (UCT) Computational Biology Group and will take place at the UCT Medical School. The computer training lab is on the basement of the Anatomy building (Teaching lab 1), accessible from Anzio Road, Observatory.


The African Centre for Gene Technologies in collaboration with the University of Cape Town’s Computational Biology Group will host this workshop at no cost to researchers who require training in NGS data analysis. Note, catering will not be provided for the course, but the medical school has two cafeterias where participants can purchase refreshments. The workshop is open to all researchers. Admission is competitive and will be based on the strength of your application.

Each applicant is required to submit a detailed motivation outlining how the course will contribute to their current research. Preference will be given to those who have already generated data which requires further analysis.

Applications should be submitted by the 17th of September 2013. Applications that are late or incomplete will not be considered. All applicants will be notified as to the outcome of their application by the 27th September 2013.


Are you a life scientist who needs to do complex analysis on large datasets?

Galaxy is an open, web-based platform for data intensive life science research that enables non-bioinformaticians to create, run, tune, and share their own bioinformatic analyses.

This hands-on workshop will teach participants how to integrate data, and perform simple and complex analysis within Galaxy. It will also cover data visualization and visual analytics, and how to share and reuse your bioinformatic analyses, all from within Galaxy.

No programming or Linux command line experience is required.


Monday through Thursday are aimed at biologists, while Friday is aimed at computer scientists.

Please note that all successful applicants (with the exception of the computer scientists) are required to attend the course from Monday to Thursday. This is non-negotiable due to the limited number of spaces available.

While day 5 (Friday) is aimed at the computer scientist, biologists attending the course are encouraged to attend the sessions on Friday. If you wish to attend the session on Friday, please indicate so when prompted during the application process.

Computer scientists wishing to attend the course on Friday also need to follow the application process.

This agenda is tentative and should be considered a work in progress.



  • Project Introduction
  • Introduction to Using Galaxy
    • Basic examples introducing the Galaxy nterface and highlighting a wide range of Galaxy's functionality.
  • Next Generation Sequencing (NGS) Data Quality Control
    • Options for evaluating quality, trimming data, and tradeoffs involved.
  • RNA-Seq Analysis Example, Part I
    • Read Mapping and Transcript Prediction using the Tuxedo Suite of Tools


  • RNA-Seq Analysis Example, Part II
    • Differential Expression Analysis with the Tuxedo Suite of Tools
  • RNA-Seq Analysis Example, Part III
    • RNA-Seq Analysis with a different set of tools
      Evaluate and discuss alternatives and selecting different approaches for different situations.

  • SNP and Variant Calling, Part I
RNA-Seq Slides


  • SNP and Variant Calling, Part II
  • ChIP-Seq Analysis
ChIP-Seq Slides


  • Genome Assembly
  • Install your own Galaxy on Amazon Web Services


  • Customizing Galaxy
  • Galaxy Tool Shed
  • Wrapping your own tools.

UCT and South African Galaxy Resources

There are 2 local Galaxy instances that may be available to course participants:

  • For UCT Staff and Students:

    • An installation on the UCT HPC cluster.  Register here.
      Please ask Gerrit if you have problems registering.

    For researchers in South Africa: 

    • An installation on the CHPC cluster.  Register here.
      Contact Dane Kennedy <dkennedy1 AT csir DOT co DOT za> for support.


2013 South Africa Galaxy Workshop Tour

Amazon Web Services

This workshop is generously supported by an AWS in Education grant award, and the University of Pretoria and the University of Cape Town. This workshop is part of the 2013 South Africa Galaxy Workshop Tour.


Contact Nicola Mulder <nicola DOT mulder AT uct DOT ac DOT za>, Gerrit Botha <gerrit AT cbio DOT uct DOT ac DOT za> or Galaxy Outreach <outreach AT galaxyproject DOT org>.