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Working with Pathogen Genomes

19-24 January 2014

Wellcome Trust Genome Campus, Hinxton, UK

Now closed for applications. Please email to join our mailing list.

This five-day workshop aims to give molecular microbiologists a working knowledge of genomic analysis, which will cover the handling and processing of DNA sequence and transcriptomic data produced by ‘second generation’ sequencers. The course will be taught by members of the Pathogen and Parasite Genomics teams from the Wellcome Trust Sanger Institute 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 small eukaryotic pathogens.

The course 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, genome annotation and differential expression analysis using RNA-seq data. 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.


Introduction to Artemis/ACT and comparative genomics

  • Using Artemis as a sequence analysis tool for prokaryote and small 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
  • Using web based sequence analysis tools

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 and RNA-seq data
  • Identifying differentially expressed genes using RNA-seq data

General bioinformatics skills

  • Introduction to the UNIX operating system
  • Basic Perl programming for processing genomic data

How to apply


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

The course tuition fees are subsidised by the Wellcome Trust for scientists based in non-commercial institutions anywhere in the world. This is a residential course and there is a registration fee of £675 towards board and lodging for non-commercial applicants. The fee for commercial applicants is £2000.

Limited bursaries are available for academics (50% of fee) and are subject to open competition.

Now closed for applications. Please email to join our mailing list.

Wellcome Trust, Gibbs Building, 215 Euston Road, London NW1 2BE, UK T:+44 (0)20 7611 8888