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PREPRINT: A Framework for Scalable Genome Assembly on Clusters, Clouds, and Grids

By Christopher Moretti, Andrew Thrasher, Li Yu, Michael Olson, Scott Emrich and Douglas Thain

Abstract

Abstract—Bioinformatics researchers need efficient means to process large collections of genomic sequence data. One application of interest, genome assembly, has great potential for parallelization, however most previous attempts at parallelization require uncommon high-end hardware. This paper introduces the Scalable Assembler at Notre Dame (SAND) framework that can achieve significant speedup using large numbers of commodity machines harnessed from clusters, clouds, and grids. SAND interfaces with the Celera open-source assembly toolkit, replacing two independent sequential modules with scalable parallel alternatives: the candidate selector exploits distributed memory capacity, and the sequence aligner exploits distributed computing capacity. For large problems, these modules provide robust task and data management while also achieving speedup with high efficiency. We show results for several datasets ranging from 738 thousand to over 320 million alignments using resources ranging from a small cluster to more than a thousand nodes spanning three institutions

Topics: Index Terms—C.2.4 Distributed Systems, Bioinformatics, Genome assembly
Year: 2013
OAI identifier: oai:CiteSeerX.psu:10.1.1.363.2464
Provided by: CiteSeerX
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