Molecular quality assurance methods for use in sequencing

1. A method of determining the complexity of a nucleic acid template, or of identifying a true sequence variant, comprising:

i) providing a nucleic acid template;

ii) providing a plurality of primer pairs, comprising a first primer and a second primer, wherein the first primer comprises a sequence complementary to a portion of the nucleic acid template, and the second primer comprises a sequence complementary to a portion of the complement of the nucleic acid template;

iii) attaching a codeword to the 5′ end of the first primer, the 5′ end of the second primer, or both, to form a codeword-primer molecule, or to the nucleic acid template to form a codeword-template molecule;

iv) performing an amplification reaction with the paired codeword-primer molecules and the nucleic acid template or with the primer pairs and the codeword-template molecule for a defined number of cycles to obtain an amplification reaction product;

v) obtaining the sequence of the amplification reaction product at the end of each cycle, at the end of the defined number of cycles, or at an intermediate number of cycles;

vi) determining the abundance of each codeword present in the amplification reaction product at the end of each cycle, at the end of the defined number of cycles, or at an intermediate number of cycles;

vii) calculating an observed codeword entropy of each cycle after step vi); and

viii) comparing the observed codeword entropy to an estimated codeword entropy, to determine the complexity of the nucleic acid template; or

ix) performing a supervised classification method based on the results of steps vi) and vii), to identify the true sequence variant.

2. The method of claim 1 wherein the true sequence variant is a low prevalence sequence variant.

3. The method of claim 1 wherein the nucleic acid template is a DNA template.

4. The method of claim 1 wherein the codeword-primer molecule or the primer is further attached to an adapter sequence.

5. The method of claim 1 wherein a different codeword is attached to each primer in the primer pair or the same codeword is attached to each primer in the primer pair.

6. The method of claim 1 wherein the codewords are attached to the nucleic acid template at random.

7. The method of claim 1 wherein the observed codeword entropy is calculated by Shannon entropy, the Simpson index, or any other diversity index.

8. The method of claim 1 wherein the codewords are present in a non-uniform pool or are present in a balanced pool.

9. The method of claim 1 further comprising determining one or more of amplification process, contamination, sample identity mismatch, or codeword pool imbalance.