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As mentioned Aseprite has a linux build.
Pixelorama is very similar to Aseprite, but has free builds. Is built with Godot and is open source.
It looks like Aseprite can export a texture atlas, but I haven't seen the ability to do so in Pixelorama.
For lighting effects there's an application called Sprite Lamp (also has a linux build) that's been around for a long time. I haven't used this one though.
I haven't done any of these workflows in awhile but I hope that this helps.
Yep, was just watching a video posted on !c/godot that had highlighted Pixelorama:
Aseprite was forked as Libresprite due to the constraints of Aseprites licensing if you're looking for a free option: https://libresprite.github.io/#!/
Aseprite I believe has a Linux build. Paid software but worth every penny.
Seconded. Aseprite is incredible, and has generally become the main tool I make game assets in.
There's libresprite