Elixir Training: Plant Genome Assembly and Annotation
The course is aimed at researchers interested in learning more about genome assembly and annotation
Du 24-09-2018 au 28-09-2018 à Cirad Montpellier
Date limite d'inscription: 15-07-2018

 

 

ABOUT

ELIXIR-FR in collaboration with IFB and CIRAD are pleased to announce a Plant Genome Assembly and Annotation event.

 

Fee

There is no course attendance fee. The participants will need to bear their travel and hotel (if any). ELIXIR-FR, Cirad and Agropolis will cover coffee breaks and lunches costs.

 

Instructors

 

Mahesh Binzer-Panchal - ELIXIR-Sweden, NBIS, Uppsala University, Sweden
Christophe Klopp - ELIXIR-France, MIAT, INRA Toulouse
Erik Hjerde - ELIXIR-Norway, , UiT The Arctic University of Norway, Norway
Joelle Amselem - ELIXIR-France, INRA - Unité de Recherche en Génomique-Info, France
Lucile Soler - ELIXIR-Sweden, NBIS, Science for Life Laboratory, Uppsala University, Sweden
Jacques Dainat - ELIXIR-Sweden, NBIS, Science for Life Laboratory, Uppsala University, Sweden
Laurent Bouri - ELIXIR-France, French Insitute of Bioinformatics UMS3601-CNRS, Université Paris-Saclay France
Victoria Dominguez Del Angel, TrC Elixir-France, French Insitute of Bioinformatics UMS3601-CNRS, Université Paris-Saclay, France
Stephanie Bocs - Elixir-France, South Green Team, CIRAD, Montpellier, France

 

Local organisers

Stephanie Bocs, Elixir-France, South Green Team, CIRAD, Montpellier, France

Victoria Dominguez Del Angel, TrC Elixir-France, French Insitute of Bioinformatics UMS3601-CNRS, Université Paris-Saclay, France  

 

Description

The course is aimed at scientists interested in learning more about plant genome assembly and annotation. It will include information useful for both the beginner and the more advanced user. We will start by introducing general concepts and then continue step-by-step to describe all major components of a genome assembly and annotation workflow, from raw data all the way to a final assembled and annotated genome. There will be a mix of lectures and hands-on practical exercises using command line Linux. After the course the participants will be aware of common practices and commonly used tools and be know how to run assembly and annotation projects.

 

 

Preliminary Programme

Time Activity

DAY 1

 

09.00 - 09.30

Welcome and introduction of teachers and round of presentation by participants

09.30 - 12.30

Session 1: Read QC - Quality Assessment of sequencing data

14.00 - 18.00

Session 2: Illumina assembly

DAY 2

 

09.00 - 12.30

Session 3: Long reads Assembly

14.00 - 18.00

Session 4: Assembly validation

DAY 3

 

09.00 - 12.30

Session 5: Structural annotation with Eugene

14.00 - 18.00

Session 6: Discussion, potentially working with the participants own data

DAY 4

 

09.00 - 12.30

Session 7: Structural annotation with Maker

14.00 - 18.00

Session 8: Functional annotation

DAY 5

 

09.00 - 12.30

Session 9: Identification of Transposable elements

14.00 - 17.00

Session 10: Manual curation

 

Learning Objectives:

  • Improve your knowledge of plant genomics (complexity)
  • Discuss current or future sequencing projects
  • Understand the difficulties of assembly, know assembly workflows, metrics provided by tools and practice
  • Know different annotation workflows of genes encoding proteins, evaluate the quality of the results, identify the technological issues and practice
  • Know different transposable element annotation workflows, evaluate the quality of the results, identify the technological issues and practice

Prerequisites

  • Knowledge in bioanalysis (Blast)
  • Basic genomic knowledge
  • Basic linux command line knowledge
  • Practice of English

 

ABOUT

We will accept a maximum of 20 participants. Priority will be given to candidates from Elixir- France and ELIXIR nodes. Notifications of acceptance will be sent shortly after the application, which will remain open until we reach 20 participants.

To register use this Link: https://www.eventbrite.fr/e/elixir-training-plant-genome-assembly-and-annotation-tickets-45929126253

 
 
 

Venue

UMR AGAP - Cirad
Lavalette 3-159 / Bât. 3 - salle 159
389 Avenue Agropolis
34398 Montpellier

 

MAP

 

 

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