If it's only 20 Loci I would do PCR and Amplicon sequencing. (Well, depends on the size of the Loci). You could use multipliex identifiers of any length which you incorporate into the amplification primer. With that amount of samples you could also think about a multiplex PCR amplifying 10 or even 20 PCR products in one reaction: that would lead to one PCR per sample targetted sequencing: I don't think anyone can do it cheaper...
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