Structural variations in genome could be more critical than SNP (Single-Nucleotide Polymorphism) in causing tumor cells, immune system diseases and fatness. It is necessary and important to detect structural variations with next generation sequencing data by means of efficient and accurate algorithms. This paper introduced a new algorithm using k-mers (short fragments of genome), string algorithms and graph algorithms, which combines similarity check, variation detection with sequence assembly. Our results showed that our method has high accuracy and it is more reliable than methods using reference and more efficient than popular algorithms.