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SeqAhead: NGS current challenges and data analysis for plant researchers

Date: Monday 19 to Friday 23 May 2014

Scientific Organiser: Vicky Schneider, The Genome Analysis Centre (TGAC), UK

Event Organiser:

  • Matt Drew, The Genome Analysis Centre (TGAC), UK

Course Faculty:

  • Bernardo Clavijo, The Genome Analysis Centre (TGAC), UK
  • Frederik Coppens, VIB, Belgium
  • Keywan Hassani-Pak, Rothamsted Research, UK
  • Richard Leggett, The Genome Analysis Centre (TGAC), UK
  • Mirko Moser, Research and Innovation Centre, Italy
  • Emily Pritchard, EMBL-EBI, UK
  • Richard Smith-Unna, University of Cambridge, UK
  • Michela Troggio, Research and Innovation Centre, Italy

Venue: The Genome Analysis Centre (TGAC)

Registration now closed

Participation: Open application with selection process



Registration fee is £100 which is payable upon an accepted application for participation on this course.

Each successful applicant will receive up to €1000 reimbursement as a part of the COST grant system to cover your travel and accommodation expenses.

Please note this is only available for participants from within the EU.

Accommodation has already been booked and details of how to pay the hotel will be given shortly after confirmation of your place.



Click here to download the programme


Course Materials

Day 1

Frederik Coppens - NGS for Plants Current Challenges

Richard Leggett - Primary and Secondary Analysis of all raw sequence data

Day 2

Bernardo Clavijo - Assembling Plant Genomes

Richard Smith-Unna - Annotating the Genome

Day 3

Mirko Moser - Genome Composition

Keywan Hassani-Pak - Plant Databases

Emily Pritchard - Browsing the Plant Genomes

Day 4

Michela Troggio - Interpreting Genomic Data

Keywan Hassani-Pak - Comparative Genomics

Day 5

Richard Smith-Unna - Optimising de novo assembly of plant transcriptomes from short sequencing reads


What is this workshop about?

The course will combine lectures and led discussions to identify key challenges, opportunities and bottlenecks, with practical session on:

  • Automated and standardized data analysis for plant species data
  • Data quality checks
  • Estimation of reproducibility
  • Batch effects
  • Statistical concepts
  • Importance of standards
  • Data formats
  • Data integration


What will I learn?

  • To discuss and reflect on best practice of experimental design and control for using NGS technologies in their context of addressing biological questions
  • Identify key challenges, opportunities and bottlenecks
  • Offering a platform for discussion and exploration of the challenges in plant research with a particular emphasis for agri-bioinformatics

Target Audience:

This course is aimed at PhD students and early stage researchers who are working or planning to engage in plant research.

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