documentation :: some comments

[EricDeveaud]

Hello,

https://mikado.readthedocs.io/en/stable/Tutorial/ have some formating problems.
code blocks are truncated in some places or misses \.

https://mikado.readthedocs.io/en/stable/Tutorial/Daijin_tutorial/#preparation-of-the-input-data
wget comamnd line to obtain Aedes_aegypti.fasta.gz is broken, generate an ERROR 400: Bad Request.

https://mikado.readthedocs.io/en/stable/Tutorial/Daijin_tutorial/#required-software may benefit to document

• gnuplot (required by samtools plot-bamstats)
• bgzip
• blast+

section Mikado miscellaneous scripts
mikado util no longer provides merge_blast and collect_compare is not documented.

section 7.4.2. Included scripts
some scripts from utils dir are not documented.

analyse_metrics.py
calculate_distances.py
create_model.py
extract_promoter_regions.py
extract_test_case.py
plac_runner.py 
remove_utrs.py

Anyway thanks for providing this extensive documentation that allow achieve the installation and testing.

regards

Eric