Add new informations: Helixer, compleasm and OMArk

topics/genome-annotation/tutorials/introduction/slides.html

@@ -161,7 +161,7 @@
 - Integration of evidence and *ab initio* predictions
 - "Consensus" of multiple sources
 - Automated pipelines
-  - [**Maker**]({% link topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.md %}), **Braker**, [**Funannotate**]({% link topics/genome-annotation/tutorials/funannotate/tutorial.md %}), **Pasa**, **Prokka**, ...
+  - [**Maker**]({% link topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.md %}), **Braker**, **Braker3**, [**Funannotate**]({% link topics/genome-annotation/tutorials/funannotate/tutorial.md %}), **Helixer** **Pasa**, **Prokka**, ...
   - Align evidences (or use pre-aligned)
   - Run *ab initio* predictors
   - Reconciliate gene models
@@ -203,6 +203,28 @@
 
 ---
 
+### Evaluation of annotation: Compleasm
+
+* A faster and more accurate reimplementation of BUSCO
+* Expected to be found in a good annotation
+* 
+* Similar results to BUSCO:
+  * Found genes
+  * Fragmented genes
+  * Duplicated genes
+
+---
+
+### Evaluation of proteome: OMArk
+
+* Assign proteins to HOGs using k-mer composition
+* HOG = Hierarchical Orthologous Groups (gene families from OMA db)
+* Differences vs BUSCO:
+  * Completeness: also considers conserved genes in multiple copies
+  * Consistency: checks if (all) proteins matches the selected lineage or not
+
+---
+
 ### Visualisation of Results
 
 Genome Browsers (JBrowse, UCSC, ...)
@@ -223,6 +245,7 @@
   - [RepeatMasker]({% link topics/genome-annotation/tutorials/repeatmasker/tutorial.md %})
   - RepeatModeler
   - REPET
+  - Red
 - Databases of repeated elements
   - Can be used by pipelines
   - Dfam
@@ -252,6 +275,14 @@
 
 ---
 
+### Helixer
+
+- Annotation based on the development and use of a cross-species deep learning model
+- Ab-initio annotation of core genes between species of large eukaryotic genomes
+- Model capable of differentiating between different intergenic regions
+
+---
+
 ## Manual Annotation
 
 - Recruit experts of some gene families
@@ -382,6 +413,7 @@
 
 ---
 
+
 ### Orthology
 
 - For each annotated gene