Improve GET_HOLOGUES episode

[Czirion]

EVALUATE THE OBJECTIVE OF USING GET_HOMOLOGUES (Does it do the same as Roary? Ot gould be easier to use Roary)

1) The questions should be something that the student could be asking, and the tool that you are teaching would give the answer. Look at the questions in the previous episodes to give you an idea of how to write your questions.

2) If the 1st figure is from the research article, maybe you can not use it unless it has a compatible-licence.

3) Use directory instead of folder.

4) Show an example of the gene family in the core with single-copy proteins, that the user may want to use for a phylogeny.

5) It is not well explained that first, you do the analysis with 5 genomes and then with 6. It should be better explained or do everything with the six genomes from the beginning. With this desition improve the Exercise 3 and give it a title.

6) The Step 4 figures show 6 genomes instead of 5. Decide how to improve this according to the issue 5). Also in the code you only generate the second figure. Something is wrong there. Both images are described as core genome. There must be a mistake since there should be core genome graph and a pangenome graph.

7) More explanation needed about opening the tree in Microreact.

8) Shorten the output of the help menu

9) Be more explanatory in the first Notes box, and give it a title

10) Explain what is a symbolic link and why you are doing it

11) The things that are an in boxes of Notes during the steps of the pipeline should be in the normal text, maybe in bold, but not in boxes.

12) Explain that the gene clusters are the same as the gene families.

13) Improve the Exercise 1. Give all the solutions and put the output of the command.

14) Explain more the Step 4. Explain the output or omitt it and just say which is the created new file.

15) Use the correct names for the images and add alternative text

16) Explain what you mean to do in the step 5 (i.e what dos it mean to obtain a pangenome matrix?)

17) use more meaningful Key Points

[Czirion]

Hacer junto con Marisol

[solnavss]

Issues in progress:

• [x] Elaborate on new episode questions
• [x] Remove "Steps" and information that is not longer used
• [x] Add Claudia's section that generates the input for PPanGGOLiN @Czirion
• [x] Change intention: from recomendation to examples
• [ ] Describe GET_HOMOLOGUES workflow using a custom diagram
• [ ] Verify paths and outputs
• [ ] Describe the relevant options when program help is displayed
• [ ] Describe the options used when running the OMCL algorithm
• [ ] Comment something about the output box after running the program
• [ ] Write a more detailed interpretation of Tettelin fits graphs
• [ ] Exercise 1: Practical, Explore Get_Homologues outputs, linked with Haydeé families (singletons, duplicated, etc)
• [ ] Exercise 2: Biological, Interpretation of distant clusters with potential outgroups

[Czirion]

How to predict gene families is going to be explained in the Manual pangenome episode

[Czirion]

Make final version of code