soaking nuts?

i work at an organic cafe and was talking with my boss the other day about soaking nuts for dips and other raw dishes. she made a comment about soaking nuts at a certain temperature to avoid foodbourne illness, but i've never read or seen anything about this (nor have i ever really bothered to look) so i thought i'd ask you all! do nuts need to be soaked in a certain way? or is it ok to throw em in a tupperware container and let them sit on the counter for a day or two at room temp?

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