May I suggest ...

[evezeyl]

Hi,
This is great :) a lot here...and already nicely described
I have some suggestions for improvements, to make your pipeline more widely usable (ie without reading all the details for the different programs)

1. improving program specific settings. Mentioning ie which program those settings correspond for all (ie Fitlong) with a redirect to the text (ie I am ie not familiar with the use of params.target_bases ... ) eg same way as you do for unicycler +

• ie. some more info or links so we can setup the data corresponding to params.*db: Path to each database for each respective program. (a list?)

2. Maybe a FAQ section in your wiki (sure will be many questions you will have to answer ... then you can put maybe questions and examples that have been asked to help users).

3. A reference list of all the papers, programs to cite - including yours - that can ie be downloaded (and added to citation manager) - maybe depending on tracks used?