PMSGA: A FAST DNA FRAGMENT ASSEMBLER

摘要

The DNA fragment assembly is an essential step in DNA sequencing projects. Since DNA sequencers output fragments, the original genome must be reconstructed from these small reads. In this paper, a new fragment assembly algorithm, Pattern Matching based String Graph Assembler (PMSGA), is presented. The algorithm uses multipattern matching to detect overlaps and a minimum cost flow algorithm to detect repeats. Special care was taken to reduce the algorithm's run time without compromising the quality of the assembly. PMSGA was compared with well-known fragment assemblers. The algorithm is faster than other assemblers. PMSGA produced high quality assemblies with prokaryotic data sets. The results for eukaryotic data are comparable with other assemblers.