Start a wiki

[SWittouck]

Make a "quick start" section in the main README file and move demonstrations of more complicated analyses to a GitHub wiki.

Example of a more complicated analysis to explain in the wiki: creating a pangenome profile database for a hierarchical pangenome (see LEGEN pipeline for a detailed example):

1. Gather the pseudogenome sequences with the fetch module.
2. Build the profile database using the pseudopangenome (part of the hierarchical pan module output) and the pseudogenome sequences.

[SWittouck]

In the wiki, the input and output files of all modules should be explained in detail.

E.g., the output of the hierarchical pan module:

• speciespangenomes: species-level orthogroups of all genes
• pseudogenomes.tsv: representative genes of species-level orthogroups; format structured in such a way that representative sequences can be gathered with the fetch module
• pseudopangenome.tsv: pangenome of the pseudogenomes
• pangenome.tsv: overall pangenome