Pan African Bioinformatics Network for H3Africa

Working with Pathogen Genomes Workshop 23-28 November 2014

Location: Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi

Deadline for applications: 5 September 2014

This five-day workshop aims to give molecular microbiologists working with bacteria and eukaryotic pathogens a working knowledge of genomic analysis, which will cover the handling and processing of DNA sequence data produced by ‘second generation’ sequencers. The workshop will be taught by members of the Pathogen and Parasite Genomics teams from the Wellcome Trust Sanger Institute and members of the Malawi-Liverpool-Wellcome Trust Clinical Research Programme, and will take the form of a series of modules covering most aspects of sequence analysis and exploitation. Each module will be introduced with a short talk, followed by hands-on worked examples using data from bacterial and eukaryotic pathogens.

The workshop begins with training in the use of genome analysis software (Artemis and ACT), developed at the Sanger Institute for genome exploration and comparative genomics. It then goes on to cover the mapping of Illumina sequence data, SNP calling, genome assembly, and genome annotation. The course also features a module that aims to teach the basics of using genome/gene sequences to plot phylogenetic relationships between microbes, as well as an introduction to scripting for basic processing and mining of data.

PLEASE NOTE: The workshop is open to applicants based in African institutes. Travel bursaries are available to attend, see below for details.


Introduction to Artemis/ACT and comparative genomics

  •     Using Artemis as a sequence analysis tool for prokaryote and eukaryotic genomes
  •     Extensive hands on experience of the Artemis genome Comparison Tool (ACT)
  •     Overview of genome sequencing strategies, assemblies and genome analysis
  •     Understanding DNA sequence data formats

Analysis of genomic sequencing data

  •     Mapping Illumina sequence data against a reference genome
  •     Genome-wide phylogenetic analysis using SNPs
  •     De novo genome assembly from short reads
  •     Annotating your genome assembly using ab initio gene finders

General bioinformatics skills

  •     Introduction to the UNIX operating system
  •     Introductory scripting for processing genomic data

How to apply

Applicants should have a molecular biology background and currently be engaged in relevant research in African institutes.

There is no workshop fee for academics/clinicians as all workshop costs will be met by The Wellcome Trust. Commercial applicants should contact us for the commercial fee.

Bursaries are available for clinical and academic applicants to cover travel, accommodation and sustenance costs and are subject to open competition.

Application forms for this workshop can now be completed online. Please click here to be redirected to the application portal. If you have any problems with the online application process, please This email address is being protected from spambots. You need JavaScript enabled to view it. us.

Please note: Applications must be supported by a recommendation from a scientific sponsor. This can be your supervisor or head of department. A request for a supporting statement will be sent to your nominated sponsor automatically during the application process. Applicants must ensure that their sponsor provides this supporting statement by the application deadline.

Deadline for applications: 5 September 2014

The original Wellcome Trust workshop call can be found here.