Ask the victim to describe the assailants crotch area etc. and cross check.
DNA tests if the guy was stupid enough not to wear a condom (but this was Assagne).
Corresponding physical injuries or bruises as described by the victim on the assailants body (there's almost always a struggle in a rape).
Clothing with traces of the victim for example hair samples from a jacket, shoe or clothing unlikely to be rinsed(in case he claims that they have never met).
Trace biological evidence on the scene (can be faked though).
Interrogation. (even very smart people tend to slip up)
Standard investigations (alibis blah blah the entire detective book routine)
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I think that the real problem is that it takes too long to verify for the 24 hour news cycle unlike a murder.