System Maintenance:
There may be intermittent impact on performance while updates are in progress. We apologize for the inconvenience.
By Topic

Assembling genomes on large-scale parallel computers

Sign In

Cookies must be enabled to login.After enabling cookies , please use refresh or reload or ctrl+f5 on the browser for the login options.

Formats Non-Member Member
$31 $13
Learn how you can qualify for the best price for this item!
Become an IEEE Member or Subscribe to
IEEE Xplore for exclusive pricing!
close button

puzzle piece

IEEE membership options for an individual and IEEE Xplore subscriptions for an organization offer the most affordable access to essential journal articles, conference papers, standards, eBooks, and eLearning courses.

Learn more about:

IEEE membership

IEEE Xplore subscriptions

4 Author(s)
Kalyanaraman, A. ; Dept. of Electr. & Comput. Eng., Iowa State Univ., Ames, IA, USA ; Emrich, S.J. ; Schnable, P.S. ; Aluru, S.

Assembly of large genomes from tens of millions of short genomic fragments is computationally demanding requiring hundreds of gigabytes of memory and tens of thousands of CPU hours. New gene-enrichment sequencing strategies are expected to further exacerbate this situation. In this paper, we present a massively parallel genome assembly framework. The unique features of our approach include space-efficient and on-demand algorithms that consume only linear space, and heuristic strategies that reduce the number of expensive pairwise sequence alignments while maintaining assembly quality. As part of the ongoing efforts in maize genome sequencing, we applied our assembly framework to the largest available collection of maize genomic data. We report the partitioning of more than 1.6 million fragments of over 1.25 billion nucleotides total size into genomic islands in 2 hours on 1,024 processors of an IBM BlueGene/L supercomputer.

Published in:

Parallel and Distributed Processing Symposium, 2006. IPDPS 2006. 20th International

Date of Conference:

25-29 April 2006