The advantages of using electroporation are the higher efficiency, more colonies, and much faster transformations compared to heat shock method.
Transformation efficiencies for electroporation are 5.0 x 109 – 2.0 x 1010 CFU/µg DNA, whereas the efficiencies for heat shock transformation are 1.0 x 105 – 2.0 x 109 CFU/µg DNA (Aune & Aachmann, 2010). Therefore, electroporation is helpful when you have to construct DNA libraries.
The drawback of this method is that you must have an electroporator, which is a special piece of equipment. In addition, the common problem during electroporation is the presence of salts or air bubbles in your DNA, and in the cuvette, can cause an arcing. Unfortunately, this will make you lose your sample and require you to redo your ligation reaction.