J. Blazewicz, B. Bosak, P. Gawron, M. Kasprzak, K. Kurowski, T. Piontek,
A. Swiercz
"Highly efficient parallel approach to the next-generation DNA sequencing"
Lecture Notes in Computer Science 7204 (2012) 262-271.
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— The final publication is available at Springer via
http://dx.doi.org/10.1007/978-3-642-31500-8_27
Abstract:
Due to the rapid development of the technology, next-generation
sequencers can produce huge amount of short DNA fragments
covering a genomic sequence of an organism in short time. There is a
need for the time-efficient algorithms which could assembly these fragments
together and reconstruct the examined DNA sequence. Previously
proposed algorithm for de novo assembly, SR-ASM, produced results of
high quality, but required a lot of time for computations. The proposed
hybrid parallel programming strategy allows one to use the two-level hierarchy:
computations in threads (on a single node with many cores)
and computations on different nodes in a cluster. The tests carried out
on real data of Prochloroccocus marinus coming from Roche sequencer
showed, that the algorithm was speeded up 20 times in comparison to
the sequential approach with the maintenance of the high accuracy and
beating results of other algorithms.
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29 Mar 2012