A framework for scalable genome assembly on clusters, clouds, and grids

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

Research output: Contribution to journalArticlepeer-review

12 Scopus citations

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 data sets 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.

Original languageEnglish (US)
Article number6165266
Pages (from-to)2189-2197
Number of pages9
JournalIEEE Transactions on Parallel and Distributed Systems
Volume23
Issue number12
DOIs
StatePublished - Nov 26 2012

All Science Journal Classification (ASJC) codes

  • Signal Processing
  • Hardware and Architecture
  • Computational Theory and Mathematics

Keywords

  • Distributed systems
  • bioinformatics
  • genome assembly

Fingerprint Dive into the research topics of 'A framework for scalable genome assembly on clusters, clouds, and grids'. Together they form a unique fingerprint.

Cite this