A method for determining a sequence of at least one target template nucleic acid molecule comprising: (a) providing a pair of samples, each sample comprising at least one target template nucleic acid molecule; (b) sequencing regions of the at least one target template nucleic acid molecule in a first of the pair of samples to provide non-mutated sequence reads; (c) introducing mutations into the at least one target template nucleic acid molecule in a second of the pair of samples to provide at least one mutated target template nucleic acid molecule; (d) sequencing regions of the at least one mutated target template nucleic acid molecule to provide mutated sequence reads; (e) analysing the mutated sequence reads, and using information obtained from analysing the mutated sequence reads to assemble a sequence for at least a portion of at least one target template nucleic acid molecule from the non-mutated sequence reads; wherein step (e) comprises preparing an assembly graph, wherein the assembly graph comprises nodes computed from non-mutated sequence reads, and each valid route through the assembly graph comprising the nodes represents the sequence of at least a portion of at least one target template nucleic acid molecule; wherein using information obtained from analysing the mutated sequence reads to assemble a sequence for at least a portion of at least one target template nucleic acid molecule from the non-mutated sequence reads comprises identifying nodes that form part of a valid route through the assembly graph using information obtained by analysing the mutated sequence reads; and wherein identifying nodes that form part of a valid route through the assembly graph using information obtained by analysing the mutated sequence reads comprises: (i) computing nodes from non-mutated sequence reads; (ii) mapping the mutated sequence reads to the assembly graph; (iii) identifying mutated sequence reads that are likely to have originated from the same at least one mutated target template nucleic acid molecule; and (iv) identifying nodes that are linked by mutated sequence reads that are likely to have originated from the same at least one mutated target template nucleic acid molecule, wherein nodes that are linked by mutated sequence reads that are likely to have originated from the same at least one mutated target template nucleic acid molecule form part of a valid route through the assembly graph. (a) providing a pair of samples, each sample comprising at least one target template nucleic acid molecule; (b) sequencing regions of the at least one target template nucleic acid molecule in a first of the pair of samples to provide non-mutated sequence reads; (c) introducing mutations into the at least one target template nucleic acid molecule in a second of the pair of samples to provide at least one mutated target template nucleic acid molecule; (d) sequencing regions of the at least one mutated target template nucleic acid molecule to provide mutated sequence reads; (e) analysing the mutated sequence reads, and using information obtained from analysing the mutated sequence reads to assemble a sequence for at least a portion of at least one target template nucleic acid molecule from the non-mutated sequence reads; (i) computing nodes from non-mutated sequence reads; (ii) mapping the mutated sequence reads to the assembly graph; (iii) identifying mutated sequence reads that are likely to have originated from the same at least one mutated target template nucleic acid molecule; and (iv) identifying nodes that are linked by mutated sequence reads that are likely to have originated from the same at least one mutated target template nucleic acid molecule,