ccTSA: A Coverage-Centric Threaded Sequence Assembler

Collection with item attached
2012
Item details URL
http://open-repository.kisti.re.kr/cube/handle/open_repository/475745.do
DOI
10.1371/journal.pone.0039232
Title
ccTSA: A Coverage-Centric Threaded Sequence Assembler
Description
This work was supported by the Seoul National University Brain FusionProgram Research Grant. The funders had no role in study design, datacollection and analysis, decision to publish, or preparation of themanuscript.
abstract
De novo sequencing, a process to find the whole genome or the regions of a species without references, requires much higher computational power compared to mapped sequencing with references. The advent and continuous evolution of next-generation sequencing technologies further stress the demands of high-throughput processing of myriads of short DNA fragments. Recently announced sequence assemblers, such as Velvet, SOAPdenovo, and ABySS, all exploit parallelism to meet these computational demands since contemporary computer systems primarily rely on scaling the number of computing cores to improve performance. However, most of them are not tailored to exploit the full potential of these systems, leading to suboptimal performance. In this paper, we present ccTSA, a parallel sequence assembler that utilizes coverage to prune k-mers, find preferred edges, and resolve conflicts in preferred edges between k-mers. We minimize computation dependencies between threads to effectively parallelize k-mer processing. We also judiciously allocate and reuse memory space in order to lower memory usage and further improve sequencing speed. The results of ccTSA are compelling such that it runs several times faster than other assemblers while providing comparable quality values such as N50.
provenance
Made available in Cube on 2018-09-28T11:21:06Z (GMT). No. of bitstreams: 0
language
English
author
Ahn, Jung Ho
orcid
Ahn, Jung Ho/0000-0003-1733-1394
accessioned
2018-09-28T11:21:06Z
available
2018-09-28T11:21:06Z
issued
2012
citation
PLOS ONE(7): 6
issn
1932-6203
uri
http://open-repository.kisti.re.kr/cube/handle/open_repository/475745.do
Funder
교육과학기술부
Funding Program
일반연구자지원
Project ID
1345193072
Jurisdiction
Rep.of Korea
Project Name
An Integrated Solution Supporting DRAM Modeling and Performance Simulation
rights
openAccess
type
article


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