Doubt with snippy-multi reference

Question

[SushiRoll]

Hey all!

I'm running snippy-core on a set of snippy outputs. I normally run all my samples as a batch with the snippy-multi command, this time I just wanted to run snippy-core so I checked (for consistency's sake) the "runme.sh" that is normally generated by snippy-multi. In the last line (corresponding to the snippy-core command) I realised that the reference flag (--ref) uses "Sample_1/ref.fa" as value. I am now confused to whether I should use my original .gbk reference (the one that I used for Snippy) or some other thing outputted by snippy. Any help would be really appreciated!

Answer 1

[andres.firrincieli]

Maybe this could help: link

[SushiRoll]

That was exactly the answer that I needed, thank you!