Abstract: The invention generally relates to methods for sequencing a nucleic acid template from both a 5? and a 3? end in a single sequencing reaction. In certain embodiments, methods of the invention involve amplifying a nucleic acid template to produce a plurality of amplicons, splitting the amplicons into first and second portions, attaching a first oligonucleotide including a first universal primer site to a 5? end of the amplicons in the first portion, and attaching a second oligonucleotide including a second universal primer site to a 3? end of the amplicons in the second portion. The first and second primer sites may be the same or may be different. The method additionally involves pooling the first and second portions, and sequencing the pooled amplicons, thereby sequencing a nucleic acid template from both a 5? and a 3? end in a single sequencing reaction.