Theoretical Basis of a New Method for DNA Fragment Assembly in k-mer Graphs

The reduction of cost and running time provided by new generation sequencing technologies made possible the emergence of thousands of genome projects in the last few years. On the other hand, those technologies posed important computational challenges, pushing the advance of many research fields in computer science. Particularly, the de novo DNA fragment assembly, which is a fundamental stage in genome sequencing, is a complex problem that demands complex algorithms to solve it. Here, we provide a theoretical basis for the construction of a new method for de novo fragment assembly based on k-mer graphs. Our proposal encompasses many difficulties found in such problems using a unique procedure, in contrast with current methods that use several high-cost procedures to overcome the same issues. Furthermore, our approach is highly scalable since it allows the use of parallelism, being very suitable for solutions with graphics processing unit (GPU).