Parallel Assembler for Fuzzy Genome Sequence Assembly

Assembly is an NP-Hard problem, which involves comparing fragments that have a time complexity of O(n2 ). This paper presents a parallel approach for sequence assembly. The parallel technique is based on classification to group organisms by similarity rather than an embarrassingly parallel approach that requires duplication of the data across all nodes. This process of classification, based on DNA signatures, is useful in parallel assembly as it divides the problem into subtasks. The classification is followed by a fuzzy assembly of these fragments. The assembly of each tasks is achieved by using a modular approach. The parallel implementation of the assembly shows a speedup in assembly while preserving coverage of fragments.

• Type: Conference
• Year: 2008
• Where: CAINE
• Authors: Sara Nasser, Adrienne Breland, Frederick C. Harris Jr.
• Keywords: CAINE 2008, Computer Science, Parallel Approach, Parallel Assembly, Sequence Assembly