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| # 2ième école de bioinformatique AVIESAN - IFB - INSERM (EBAII 2024) | ||
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| ## Assemblage et annotation de novo de génomes | ||
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| **Du 03-06-2024 au 07-06-2024 à la Station biologique de Roscoff** | ||
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| ## Web site | ||
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| - Web pages: <https://ifb-elixirfr.github.io/EBAII/2024/Assemblage> | ||
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| From there, you can also find a link to download the whole repository with `git`. | ||
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| **** | ||
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| ## Accès à Galaxy | ||
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| Tous les TPs se feront sur [UseGalaxy.fr](https://usegalaxy.fr). Chaque participant doit se connecter à son compte personnel (à créer avant la formation). | ||
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| Pour bénéficier des ressources de calcul réservées pour cette formation, chaque participant doit : | ||
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| - se connecter sur [UseGalaxy.fr](https://usegalaxy.fr) | ||
| - cliquer sur [ce lien](https://usegalaxy.fr/join-training/ebaii_aa/) | ||
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| ## Supports de cours | ||
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| ### Cours généraux | ||
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| | Cours | Intervenants | Supports | | ||
| |-----------------------------------|----------------------|--------------------------------------------------------------------------------------------------------------------------------------------------| | ||
| | Introduction | A. Cormier; E. Corre | [Cours](https://training.galaxyproject.org/training-material/topics/assembly/tutorials/get-started-genome-assembly/slides.html) | | ||
| | Outils de séquençage | J. Kreplak | [Cours](https://docs.google.com/presentation/d/1rtTCyVF4dz0Trmny5e8r1brzfNab8ZUN/edit?usp=sharing&ouid=109813995176155673766&rtpof=true&sd=true) | | ||
| | QC des lectures | C. Klopp; O. Rué | [Cours](https://hackmd.io/EsjYvtqdQAmW9RmvKr-aaQ?view) | | ||
| | Validation d'assemblage (Théorie) | E. Corre; A. Cormier | [Cours](https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-quality-control/slides.html) | | ||
| | Validation d'assemblage (TP) | A. Cormier; E. Corre | [TP](https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-quality-control/tutorial.html) | | ||
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| ### Assemblage | ||
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| | Cours | Intervenants | Supports | | ||
| |---------------|----------------------------------|---------------------------------------------------------------------------------------------------------------| | ||
| | Assemblage | C. Klopp; D. Naquin; | [Cours](Genome_assembly.pdf) <br> [TP](Genome_assembly_tp.pdf) | | ||
| | Polishing | J.-M. Aury | [Cours](https://docs.google.com/presentation/d/1RAScBkXvWkRCuD2WAbgNLJZ8zJNXz9skkHJ-MGp4VBk/edit?usp=sharing) | | ||
| | Scaffolding | J. Kreplak; C. Klopp; A. Cormier | [Cours](https://drive.google.com/file/d/1SRBBqRPUUTePJ7K1wsqbmaFGqAuvVIt6/view?usp=sharing) | | ||
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| ### Annotation | ||
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| #### Annotation procaryotes | ||
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| | Cours | Intervenants | Supports | | ||
| |-------------------------------|--------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| | ||
| | Introduction | G. Gautreau | [1. Introduction to prokaryotic genomes annotation](https://github.com/IFB-ElixirFr/EBAII/files/9681928/1.Introduction.to.prokaryotic.genomes.annotation.pdf)| | ||
| | Dataset | H. Chiapello | [2.1 Dataset Construction](https://github.com/IFB-ElixirFr/EBAII/files/9659668/2.1-Dataset-Construction-EBAIIA.A.pdf)| | ||
| | Analyse | H. Chiapello | [2.2 Dataset Analysis](https://github.com/IFB-ElixirFr/EBAII/files/9659684/2.2-Dataset-Analysis-EBAIIA.A.pdf)| | ||
| | Déreplication | H. Chiapello | [2.3 Dataset Dereplication](https://github.com/IFB-ElixirFr/EBAII/files/9659690/2.3-Dataset-Dereplication-EBAIIA.A.pdf)| | ||
| | CDS prediction | G. Gautreau | [3. Prediction of coding genes](https://github.com/IFB-ElixirFr/EBAII/files/9681927/3.Prediction.of.coding.genes.pdf)| | ||
| | Non coding gene prediction | G. Gautreau | [4. Prediction of non coding genes](https://github.com/IFB-ElixirFr/EBAII/files/9681926/4.Prediction.of.non.coding.genes.pdf)| | ||
| | Functional annotation (intro) | G. Gautreau | [5. Introduction to functional annotation](https://github.com/IFB-ElixirFr/EBAII/files/9681925/5.Introduction.to.functional.annotation.pdf)| | ||
| | Prokka + Vizualisation | G. Gautreau | [6. and 7. Let's play with a prokaryotic annotation tool_ Prokka](https://github.com/IFB-ElixirFr/EBAII/files/9681924/6.and.7.Let.s.play.with.a.prokaryotic.annotation.tool_.Prokka_JBrowse.pdf)| | ||
| | InterScan + EggNOG | J. Joëts | [8. Functional annotation](https://github.com/IFB-ElixirFr/EBAII/files/9662567/FunctAnnot.jjoets.pdf)| | ||
| | Relational annotation (intro) | G. Gautreau | [9. Introduction to relational annotation](https://github.com/IFB-ElixirFr/EBAII/files/9681923/9.Introduction.to.relational.annotation.pdf)| | ||
| | Specialized databases/tools | G. Gautreau | [10. Discussion on specialized databases/tools](https://github.com/IFB-ElixirFr/EBAII/files/9681921/10.Discussion.on.specialized.databases.pdf)| | ||
| | Annotation plateforms | G. Gautreau | [11. Automatic annotation plateforms](https://github.com/IFB-ElixirFr/EBAII/files/9681920/_11.Automatic.annotation.plateform.pdf)| | ||
| | Conclusion | G. Gautreau | [12. Conclusion](https://github.com/IFB-ElixirFr/EBAII/files/9681919/12.Conclusion.prokaryotic.genome.annotation.pdf)| | ||
| | Introduction to pangenomic | G. Gautreau | [13. Introduction to pangenomic](https://github.com/IFB-ElixirFr/EBAII/files/9681917/13.Introduction.to.pangenomic.pdf)| | ||
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| #### Annotation eucaryotes | ||
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| | Cours | Intervenants | Supports | | ||
| |----------------------------------|---------------|----------| | ||
| | Repeat masking | J. Kreplak | [Cours](https://drive.google.com/file/d/1rcF9d7ZG4gPMrMYjt3vhwGzCGhdF2BVy/view?usp=sharing) <br> [TP](https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/repeatmasker/tutorial.html) | | ||
| | Annotation de gènes | A. Bretaudeau | [Cours](https://training.galaxyproject.org/training-material/topics/genome-annotation/slides/introduction.html)<br>[TP](https://training.galaxyproject.org/topics/genome-annotation/tutorials/funannotate/tutorial.html) | | ||
| | Visualisation | A. Bretaudeau | [TP](https://training.galaxyproject.org/topics/genome-annotation/tutorials/funannotate/tutorial.html#visualisation-with-a-genome-browser) | | ||
| | ARN long non-codants | S. Robin | [Cours](FEELnc_Sept_2022.pdf)<br>[TP](https://training.galaxyproject.org/topics/genome-annotation/tutorials/lncrna/tutorial.html) | | ||
| | BUSCO | S. Robin | [Cours](BUSCO_Sept_2022.pdf)<br>[TP]() | | ||
| | Annotation fonctionnelle | J. Joëts | [Cours](https://drive.google.com/file/d/1vP2NMW0c0aOWSRHKwU3FNHzHRovg9GMp/view?usp=sharing) | | ||
| | Analyse intra- & interspécifique | J. Joëts | [Cours](https://drive.google.com/file/d/1UQuovplBzxYgk-kIw8E5dIJ-ids2yVmh/view?usp=sharing) | | ||
| | Analyse pangénomique | J. Joëts | [Cours](https://drive.google.com/file/d/1ueTV24RUvvof4rUSKv7dKRYr5HcGvarq/view?usp=sharing) | | ||
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| ### Analyses tierces | ||
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| | Cours | Intervenants | Supports | | ||
| |------------|-------------------|----------| | ||
| | Procaryote | G. Gautreau | À venir | | ||
| | Eucaryote | H. Roest Crollius | À venir | |