Parallel hierarchical adaptive genetic algorithm for fragment assembly

Fragment assembly is an important task in genome sequencing, and involves reconstructing a long sequence based on many overlapping subsequences (fragments) that contain errors. This paper presents a fragment assembler using a new parallel hierarchical adaptive variation of evolutionary algorithms. The innovative features include a new measure for evaluating sequence assembly quality and the development of a hybrid algorithm. Results from the simulation of 56 cases demonstrate that sequence assembly by the new sequencing method is highly accurate and noise-tolerant.