Alignment. You could easily automate alignment of raw sequencing reads to their position in the reference genome. From there, even variant calling (finding your individual changes from the reference) is pretty easy as well.

Assembly is a bigger challenge that takes the raw reads and puts them together into a larger (graph) structure. This is usually de-novo, but could be able to be done with a reference as well. But this is not really something that is routine or possible with 30X sequence coverage to the degree one would expect.

The wet-lab portion isn't terrible and anyone with skills making anything (soldering, for example), should be able to do it -- once you figured out some of the jargon.

The bigger challenge someone not trained in this would have is interpreting the variations that you'd find. This can be quite difficult to figure out if an A>C at a particular position is meaningful or not. Again, much of these can be filtered using existing tools, but even then, it can be quite difficult to interpret results.