DNA sequencing error correction using spectral alignment

Abstract

The second generation DNA sequencing technology can generate large number of DNA fragments/reads in a relatively short time. A DNA sequence assembly step is required to obtain whole genome sequences from reads. The assembly process generally uses graph based approach. This approach is very sensitive due to DNA sequencing errors. To obtain the optimal results in assembly process, the error correction step can be performed before or after the assembly process. In this research, we developed a software prototype for correcting DNA sequencing error. We employed the spectral alignment technique implemented as a pre-processing step before the DNA sequence assembly process. We tested our method by using simulated DNA reads containing errors. We measured the results by evaluating the number of nodes. The evaluation results showed that our method can reduce the complexity of graph shown by the decreasing of number of nodes. It can be stated that our method has successfully corrected DNA reads which contain sequencing errors.