A New Approach for De Bruijn Graph Construction in De Novo Genome Assembling

Fragment assembly is a current fundamental problem in bioinformatics. In the absence of a reference genome sequence that could guide the whole process, a de Bruijn Graph data structure has been considered to improve the computational processing. Notably, we need to count on a broad set of k-mers, biological sequences substrings. However, the construction of a de Bruijn Graph has a high computational cost, primarily due to main memory consumption. Some approaches use external memory processing to achieve feasibility. These solutions generate all k-mers with high redundancy, increasing the number of managed data and, consequently, the number of I/O operations. This work proposes a new approach for de Bruijn Graph construction that does not need to generate all k-mers. The solution enables to reduce computational requirements and execution feasibility.