DNA fragments are separated for sequencing using gel electrophoresis. This is a technique that separates DNA fragments based on size only.

Gel electrophoresis involves applying an electric current through a gel containing the negatively charged DNA fragments. When the electric current is applied, these negatively charged fragments move towards the positive electrode. Because all DNA fragments have the same amount of charge per mass, the smaller-sized fragments move through the gel faster than the larger-sized fragments. This allows them to be separated according to size.