Random nucleotide mutation for nucleotide template counting and assembly

A method for sequencing a nucleic acid molecule (NAM) that comprises two or more segments having substantially the same sequence, and that has a length of more than one sequencing read, comprising

• i) obtaining two or more copies of the NAM;
• ii) subjecting each copy of the NAM in step i) to a mutagenesis that mutates only select nucleic acid positions in the NAMs at a rate of 10% to 90% to produce mutated copies of the NAM (mcNAM);
• iii) amplifying each of the mcNAMs;
• iv) obtaining composite sequences of the mcNAMs that are produced by assembling sequence reads of the amplified mcNAMs, such that when taken together, span as much as possible of the entire length of the NAM, by
• a) aligning the sequence reads according to matching mutation patterns in overlaps of the sequence reads by a scoring method that assigns a weight to the overlaps in the sequence reads that reflects how unlikely it is that the overlaps agree on their mutation patterns by chance, and aligning the sequence reads by selecting overlaps that have the highest assigned weight, and
• b) mapping the composite sequences,
• thereby sequencing the NAM.