The present invention relates to methods for generating sequences of template nucleic acid molecules, methods for determining sequences of at least two template nucleic acid molecules, computer programs adapted to perform the methods and computer readable media storing the computer programs. In particular the present invention relates to methods for generating sequences of at least one individual target template nucleic acid molecule comprising: a) providing at least one sample of nucleic acid molecules comprising at least two target template nucleic acid molecules; b) introducing a first molecular tag into one end of each of the at least two target template nucleic acid molecules and a second molecular tag into the other end of each of the at least two target template nucleic acid molecules to provide at least two tagged template nucleic acid molecules wherein each of the at least two tagged template nucleic acid molecules is tagged with a unique first molecular tag and a unique second molecular tag; c) amplifying the at least two tagged template nucleic acid molecules to provide multiple copies of the at least two tagged template nucleic acid molecules comprising the first molecular tag and the second molecular tag; d) sequencing regions of the at least two tagged template nucleic acid molecules comprising the first molecular tag and the second molecular tag; and e) reconstructing a consensus sequence for at least one of the at least two target template nucleic acid molecules.
