What's the best way to encode samples?

[mvdirty]

You probably just go the best with the original wave file. Most
conversions do the same as the NerdSEQ does internally.

Very true. The NerdSEQ actually does a pretty nice conversion on most loaded samples.

In my case, I scripted a solution because I wanted to try different dithering options and sample rates for various samples, was renaming and reorganizing the files via script, and had hundreds of files to process (resulting in thousands.)

Unless in need of dithering (and/or doing a bunch of re-org) then simply loading the samples is usually fine.

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Some weeks back I wrote some code, using SoX, to help process some.... 

Hi, could you share your Sox code please? 
I'm just diving into this 8bit raw conversion and I'm having issues with zipper distortion printed over the samples..

I don’t have it in front of me at the moment but it was mostly file organization scripting with a bit of sox invocation along the way. The sox operations themselves were bog standard, setting output bit depth and sample rate, and I had the script generate variations with and without dithering. The sox docs should have the command line examples you need, but let me know if you can’t find them and I might be able to dig up the code.