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This course introduces annotation, such as structural gene annotation with EGNEP or MAKER workflows, in the Plant Genomme Assembly and Annotation course, both in a theoretical and practical way, with hands-on practice sessions. It will help you to configure and run your own pipelines using these tools through command-line interface.

MAKER2 : An annotation pipeline and genome-database management tool for second-generation genome projects. Holt, Carson; Yandell, Mark. BMC Bioinformatics, Vol. 12, No. 1, 491, 22.12.2011.

Genome Annotation in Plants and Fungi: EuGène as a Model Platform. Sylvain Foissac et al. Current Bioinformatics, 2008. DOI: 10.2174/157489308784340702

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Carver T, Harris SR, Berriman M, Parkhill J and McQuillan JA. Bioinformatics (Oxford, England) 2012;28;4;464-9 PMID:22199388

MAKER website

EuGène website




Prior knowledge on workflow execution not necessary Basic knowledge of Linux (Linux for dummies required)


  • Why using a combiner / integrator to annotate gene ?
  • How to annotate a eukaryotic genome ?
  • How to configure / to customize gene annotation workflow ?
  • How to execute them?
  • Use case

Learning objectives

  • Have revised the structure of an eukaryotic gene.
  • Learned what is annotation of eukaryotic genes.
  • Understood the major steps of a combiner like EuGene.
  • Explaining the major steps of MAKER and EuGène,
    in which way they differ from each other.
  • Annotating your genome with MAKER and EuGène.
  • Know how to Launch a virtual machine on IFB cloud.
  • Know how to configure and run MAKER VM / Eugene VM on the Arabidopsis genome.
  • Know how to Assess the results with Busco.

Training material

  • Practice Annotation MAKER : see
  • Practice Annotation Eugene : see
  • Practice Manual Curation : see


  • Jacques Dainat (JD) -
  • Lucile Soler (LS) -
  • Stéphanie Bocs (SSB) -
  • Laurent Bouri (LB) -
  • Jonathan Lorenzo (JL) -


Date Location Topics Participants Instructors Links Units
2018 Montpellier, France PGAA 22 JD, LS, SB, LB, JL Elixir GAA wiki PGAA course announcement Elixir e-learning platform IRD, Cirad, Montpellier SupAgro, INRA, IPS2, Neiker, RWTH Aachen University