PMMR: A Method for Masking Repeats in DNA Fragment Assembly

A method named PMMR (previously merging for masking repeats) is proposed in this paper for masking repeats in DNA fragment assembly. The method firstly identifies and counts the fragments including a same k-mer substring by scanning the shotgun data set. Then, it merges these fragments by the same k-mer substring. Based on merging, the method can not only mark the position of the repeats, but also reduce the scale of shotgun data set. The computer simulations show that the rate of repeats recognition is enhanced in this method, and the CPU time of DNA fragment assembly will be reduced.