Your idea is basically sound. However, rather than creating threads directly, or indirectly through some kind of ThreadManager of your own design, use an Executor from Java's concurrency package. It does everything you need, and other people have already taken the time to write and debug it. An executor manages a queue of tasks, so you don't need to worry about providing the threadsafe queue yourself either.
There's no difference between Callable and Runnable except that the former returns a value. Executors will handle both, and ready them the same.
It's not clear to me whether you're planning to make the preparation step a separate task to the analyses, or fold it into one of them, with that task spawning the other analysis task halfway through. I can't think of any reason to strongly prefer one to the other, but it's a choice you should think about.
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