Fuzzy-based Spectral Alignment for Correcting DNA Sequence from Next Generation Sequencer

Kana Saputra S (Bogor Agricultural University)
Wisnu Ananta Kusuma (Bogor Agricultural University)
Agus Buono (Bogor Agricultural University)

TELKOMNIKA (Telecommunication Computing Electronics and Control)
Vol 14, No 2: June 2016

Next generation sequencing technology is able to generate short read in large numbers and in a relatively short in single running programs. Graph based DNA sequence assembly used to handle these big data in assembly step. The graph based DNA sequence assembly is very sensitive to DNA sequencing error. This problem could be solved by performing an error correction step before the assembly process. This research proposed fuzzy inference system (FIS) model based spectral alignment method which can detect and correct DNA sequencing error. The spectral alignment technique was implemented as a pre-processing step before the DNA sequence assembly process. The evaluation was conducted using Velvet assembler. The number of nodes yielded by the Velvet assembler become a measure of the success of error correction. The results shows that FIS model based spectral alignment created small number of nodes and therefore it successfully corrected the DNA reads.