[inetknght]

That depends on the technology. The technology I most often work with will have lots of fake DNA basepairs in a soup, which has the real subject's DNA broken apart into fragments and attached to a substrate to keep it from moving. The fake DNA basepairs bind to the complementary real basepairs and emit fluorescent light when doing so. En masse, the fluorescent light gets captured on camera and each of the possible basepairs' colors are scored, to provide a call for that basepair. Repeat the cycle a few times, map the lights to the same spots, and you generate a sequence of basepair 'reads' which are then sent further down a software pipeline for later analysis.

...the later steps in the pipeline involve using lots of complex math to reassemble the sequenced fragments back together, either using a reference assembly (such as the Human Genome Project) or else de-novo assembly (which basically _builds_ a reference assembly through lots and lots and lots of effort).

There are other technologies as well which I'm not so familiar with.