DNA Synthesis Using Shortmers

In conventional DNA synthesis machines many strands are usually synthesized in parallel by iterating through a supersequence s and adding in each cycle a single nucleotide to a subset of the strands. Then, the length of s determines the number of the cycles, hence the time and the cost of the synthesis process too. Recently, in order to optimize the synthesis process, researchers have suggested to append in each cycle a shortmer instead of a single nucleotide. The present work studies this optimization from a theoretical point of view. In particular, it discusses which shortmers are the best to use, and how to calculate the number of cycles required to synthesize in parallel a set of strands using a set of shormers. Lastly, and following a previously described connection between the DNA synthesis problem and costly constrained graphs, the paper investigates calculating the capacities of such non-deterministic graphs.