content: make draft content for the latest 3 episode

_episodes/04-gene_calling_annotation.md

@@ -37,23 +37,9 @@ When you are contempt with the workflow, click save. Next, we will run the analy
 >
 {: .challenge}
 
-## antiSMASH: 
+## Busco: 
 
-> ## Discussion 02 - AntiSMASH
-> 
->
-> > ## Solution
-> >
-> > TBD
-> {: .solution}
->
-{: .challenge}
-
-## Abricate 
-ABRicate is a tool for the detection of antimicrobial and virulence genes. It is also available on Galaxy, so you don’t have to download your assembly for this. It uses different databases for example CARD to detect virulence genes in the genome. For more information: https://github.com/tseemann/abricate.  
-See below an example of default parameters with CARD database selected, an explanation of the output table and an example output. 
-
-> ## Discussion 02 - AntiSMASH
+> ## Discussion 02 - Busco
 > 
 >
 > > ## Solution

_episodes/05-genome_analysis.md

@@ -21,7 +21,7 @@ For more information:
 - https://academic.oup.com/nar/article/39/suppl_2/W339/2507123
 - https://academic.oup.com/nar/article/47/W1/W81/5481154
 
-> ## Discussion 02 - AntiSMASH
+> ## Discussion 01 - AntiSMASH
 > 
 >
 > > ## Solution
@@ -35,7 +35,7 @@ For more information:
 ABRicate is a tool for the detection of antimicrobial and virulence genes. It is also available on Galaxy, so you don’t have to download your assembly for this. It uses different databases for example CARD to detect virulence genes in the genome. For more information: https://github.com/tseemann/abricate.  
 See below an example of default parameters with CARD database selected, an explanation of the output table and an example output. 
 
-> ## Discussion 02 - AntiSMASH
+> ## Discussion 02 - Abricate
 > 
 >
 > > ## Solution

_episodes/06-Extra.md

@@ -5,9 +5,18 @@ exercises: 0
 questions:
 - "Using Command Line Tools for Bioinformatic Analysis"
 objectives:
-- "Assigning gene calls to sequence and annotate them with the known databases"
+- "Getting a gist command line tools for a more flexibility in bioinformatic analysis"
 keypoints:
-- "Genome annotation starts by identifying genes and other functional elements (rRNA, tRNA, etc.) within the nucleotides. This is followed by comparison with databases of interest to predict the functions encoded in the genes."
+- "Galaxy might not have all the tools and version required to run your analysis. Having a skill to work with command line tools and other programming language give you flexibility in your research."
 ---
 
+## Where to start
+
+## Example: Semi-automated Trycycler Assembly via Snakemake
+For Nanopore only assembly, Trycycler offer a better accuracy to generate consensus assembly (combining multiple assemblies of the same isolate). Rather than only using one assembler like we do (Flye), Trycycler can subsample our reads and build multiple assemblies using different algorithms, then make a consensus out of it. You can also find Trycycler in galaxy.eu toolbox, but as it is quite intensive, I prefer to run it on a local machine / server.
+
+Installing and running a command line tools for a newcomer might seems daunting. Nevertheless, there are two popular workflow manager: Snakemake and Nextflow, which makes running various pipelines and installing dependencies easier. We have tried to make a prototype to semi-automate run Trycycler via Snakemake here: [https://github.com/matinnuhamunada/genome_assembly_tryouts](https://github.com/matinnuhamunada/genome_assembly_tryouts). 
+
+The TAs will run it for you, but it is also quite easy to run it on your own when you have the time (and resources).
+
 {% include links.md %}