diff --git a/2024/Assembly/README.md b/2024/Assembly/README.md new file mode 100644 index 0000000..a188cb6 --- /dev/null +++ b/2024/Assembly/README.md @@ -0,0 +1,87 @@ + +# 2ième école de bioinformatique AVIESAN - IFB - INSERM (EBAII 2024) + +## Assemblage et annotation de novo de génomes + +**Du 03-06-2024 au 07-06-2024 à la Station biologique de Roscoff** + + +## Web site + +- Web pages: + +From there, you can also find a link to download the whole repository with `git`. + +**** + +## Accès à Galaxy + +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). + +Pour bénéficier des ressources de calcul réservées pour cette formation, chaque participant doit : + +- se connecter sur [UseGalaxy.fr](https://usegalaxy.fr) +- cliquer sur [ce lien](https://usegalaxy.fr/join-training/ebaii_aa/) + +## Supports de cours + +### Cours généraux + +| 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) | + + +### Assemblage + +| Cours | Intervenants | Supports | +|---------------|----------------------------------|---------------------------------------------------------------------------------------------------------------| +| Assemblage | C. Klopp; D. Naquin; | [Cours](Genome_assembly.pdf)
[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) | + +### Annotation + +#### Annotation procaryotes + +| 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)| + +#### Annotation eucaryotes + +| Cours | Intervenants | Supports | +|----------------------------------|---------------|----------| +| Repeat masking | J. Kreplak | [Cours](https://drive.google.com/file/d/1rcF9d7ZG4gPMrMYjt3vhwGzCGhdF2BVy/view?usp=sharing)
[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)
[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)
[TP](https://training.galaxyproject.org/topics/genome-annotation/tutorials/lncrna/tutorial.html) | +| BUSCO | S. Robin | [Cours](BUSCO_Sept_2022.pdf)
[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) | + + +### Analyses tierces + +| Cours | Intervenants | Supports | +|------------|-------------------|----------| +| Procaryote | G. Gautreau | À venir | +| Eucaryote | H. Roest Crollius | À venir |