ccTSA: A Coverage-Centric Threaded Sequence Assembler
Identifieur interne : 001067 ( Pmc/Curation ); précédent : 001066; suivant : 001068ccTSA: A Coverage-Centric Threaded Sequence Assembler
Auteurs : Jung Ho AhnSource :
- PLoS ONE [ 1932-6203 ] ; 2012.
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.
Url:
DOI: 10.1371/journal.pone.0039232
PubMed: 22723971
PubMed Central: 3378524
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: Pour aller vers cette notice dans l'étape Curation :001067
Links to Exploration step
PMC:3378524Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">ccTSA: A Coverage-Centric Threaded Sequence Assembler</title>
<author><name sortKey="Ahn, Jung Ho" sort="Ahn, Jung Ho" uniqKey="Ahn J" first="Jung Ho" last="Ahn">Jung Ho Ahn</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">22723971</idno>
<idno type="pmc">3378524</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3378524</idno>
<idno type="RBID">PMC:3378524</idno>
<idno type="doi">10.1371/journal.pone.0039232</idno>
<date when="2012">2012</date>
<idno type="wicri:Area/Pmc/Corpus">001067</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001067</idno>
<idno type="wicri:Area/Pmc/Curation">001067</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001067</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">ccTSA: A Coverage-Centric Threaded Sequence Assembler</title>
<author><name sortKey="Ahn, Jung Ho" sort="Ahn, Jung Ho" uniqKey="Ahn J" first="Jung Ho" last="Ahn">Jung Ho Ahn</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
</analytic>
<series><title level="j">PLoS ONE</title>
<idno type="eISSN">1932-6203</idno>
<imprint><date when="2012">2012</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p>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.</p>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Miller, Jr" uniqKey="Miller J">JR Miller</name>
</author>
<author><name sortKey="Koren, S" uniqKey="Koren S">S Koren</name>
</author>
<author><name sortKey="Sutton, G" uniqKey="Sutton G">G Sutton</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Butler, J" uniqKey="Butler J">J Butler</name>
</author>
<author><name sortKey="Maccallum, I" uniqKey="Maccallum I">I MacCallum</name>
</author>
<author><name sortKey="Kleber, M" uniqKey="Kleber M">M Kleber</name>
</author>
<author><name sortKey="Shlyakhter, Ia" uniqKey="Shlyakhter I">IA Shlyakhter</name>
</author>
<author><name sortKey="Belmonte, Mk" uniqKey="Belmonte M">MK Belmonte</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Elaine, Rm" uniqKey="Elaine R">RM Elaine</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name>
</author>
<author><name sortKey="Phillippy, Am" uniqKey="Phillippy A">AM Phillippy</name>
</author>
<author><name sortKey="Zimin, A" uniqKey="Zimin A">A Zimin</name>
</author>
<author><name sortKey="Puiu, D" uniqKey="Puiu D">D Puiu</name>
</author>
<author><name sortKey="Magoc, T" uniqKey="Magoc T">T Magoc</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Smith, Tf" uniqKey="Smith T">TF Smith</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Daniel, Rz" uniqKey="Daniel R">RZ Daniel</name>
</author>
<author><name sortKey="Birney, E" uniqKey="Birney E">E Birney</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Simpson, Jt" uniqKey="Simpson J">JT Simpson</name>
</author>
<author><name sortKey="Wong, K" uniqKey="Wong K">K Wong</name>
</author>
<author><name sortKey="Jackman, Sd" uniqKey="Jackman S">SD Jackman</name>
</author>
<author><name sortKey="Schein, Je" uniqKey="Schein J">JE Schein</name>
</author>
<author><name sortKey="Jones, Sj" uniqKey="Jones S">SJ Jones</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Li, R" uniqKey="Li R">R Li</name>
</author>
<author><name sortKey="Zhu, H" uniqKey="Zhu H">H Zhu</name>
</author>
<author><name sortKey="Ruan, J" uniqKey="Ruan J">J Ruan</name>
</author>
<author><name sortKey="Qian, W" uniqKey="Qian W">W Qian</name>
</author>
<author><name sortKey="Fang, X" uniqKey="Fang X">X Fang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Jackson, Bg" uniqKey="Jackson B">BG Jackson</name>
</author>
<author><name sortKey="Regennitter, M" uniqKey="Regennitter M">M Regennitter</name>
</author>
<author><name sortKey="Yang, X" uniqKey="Yang X">X Yang</name>
</author>
<author><name sortKey="Schnable, Ps" uniqKey="Schnable P">PS Schnable</name>
</author>
<author><name sortKey="Aluru, S" uniqKey="Aluru S">S Aluru</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wenyu, Z" uniqKey="Wenyu Z">Z Wenyu</name>
</author>
<author><name sortKey="Jiajia, C" uniqKey="Jiajia C">C Jiajia</name>
</author>
<author><name sortKey="Yang, Y" uniqKey="Yang Y">Y Yang</name>
</author>
<author><name sortKey="Yifei, T" uniqKey="Yifei T">T Yifei</name>
</author>
<author><name sortKey="Jing, S" uniqKey="Jing S">S Jing</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hennessy, Jl" uniqKey="Hennessy J">JL Hennessy</name>
</author>
<author><name sortKey="Patterson, Da" uniqKey="Patterson D">DA Patterson</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Culler, D" uniqKey="Culler D">D Culler</name>
</author>
<author><name sortKey="Singh, Jp" uniqKey="Singh J">JP Singh</name>
</author>
<author><name sortKey="Gupta, A" uniqKey="Gupta A">A Gupta</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Pevzner, Pa" uniqKey="Pevzner P">PA Pevzner</name>
</author>
<author><name sortKey="Tang, H" uniqKey="Tang H">H Tang</name>
</author>
<author><name sortKey="Waterman, Ms" uniqKey="Waterman M">MS Waterman</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Berger, Ed" uniqKey="Berger E">ED Berger</name>
</author>
<author><name sortKey="Zorn, Bg" uniqKey="Zorn B">BG Zorn</name>
</author>
<author><name sortKey="Mckinley, Ks" uniqKey="Mckinley K">KS McKinley</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Richter, Dc" uniqKey="Richter D">DC Richter</name>
</author>
<author><name sortKey="Ott, F" uniqKey="Ott F">F Ott</name>
</author>
<author><name sortKey="Auch, Af" uniqKey="Auch A">AF Auch</name>
</author>
<author><name sortKey="Schmid, R" uniqKey="Schmid R">R Schmid</name>
</author>
<author><name sortKey="Huson, Dh" uniqKey="Huson D">DH Huson</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Kelley, Dr" uniqKey="Kelley D">DR Kelley</name>
</author>
<author><name sortKey="Schatz, Mc" uniqKey="Schatz M">MC Schatz</name>
</author>
<author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Marteb, B" uniqKey="Marteb B">B Marteb</name>
</author>
<author><name sortKey="Christiaan, Vh" uniqKey="Christiaan V">VH Christiaan</name>
</author>
<author><name sortKey="Hans, Jj" uniqKey="Hans J">JJ Hans</name>
</author>
<author><name sortKey="Derek, B" uniqKey="Derek B">B Derek</name>
</author>
<author><name sortKey="Walter, P" uniqKey="Walter P">P Walter</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhang, Z" uniqKey="Zhang Z">Z Zhang</name>
</author>
<author><name sortKey="Schwartz, S" uniqKey="Schwartz S">S Schwartz</name>
</author>
<author><name sortKey="Wagner, L" uniqKey="Wagner L">L Wagner</name>
</author>
<author><name sortKey="Miller, W" uniqKey="Miller W">W Miller</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Stephen, Fa" uniqKey="Stephen F">FA Stephen</name>
</author>
<author><name sortKey="Warren, G" uniqKey="Warren G">G Warren</name>
</author>
<author><name sortKey="Webb, M" uniqKey="Webb M">M Webb</name>
</author>
<author><name sortKey="Eugene, Wm" uniqKey="Eugene W">WM Eugene</name>
</author>
<author><name sortKey="David, Jl" uniqKey="David J">JL David</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Marcais, G" uniqKey="Marcais G">G Marçais</name>
</author>
<author><name sortKey="Kingsford, C" uniqKey="Kingsford C">C Kingsford</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id>
<journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id>
<journal-id journal-id-type="publisher-id">plos</journal-id>
<journal-id journal-id-type="pmc">plosone</journal-id>
<journal-title-group><journal-title>PLoS ONE</journal-title>
</journal-title-group>
<issn pub-type="epub">1932-6203</issn>
<publisher><publisher-name>Public Library of Science</publisher-name>
<publisher-loc>San Francisco, USA</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">22723971</article-id>
<article-id pub-id-type="pmc">3378524</article-id>
<article-id pub-id-type="publisher-id">PONE-D-12-05176</article-id>
<article-id pub-id-type="doi">10.1371/journal.pone.0039232</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
<subj-group subj-group-type="Discipline-v2"><subject>Biology</subject>
<subj-group><subject>Computational Biology</subject>
<subj-group><subject>Genomics</subject>
<subj-group><subject>Genome Analysis Tools</subject>
<subj-group><subject>Sequence Assembly Tools</subject>
</subj-group>
</subj-group>
<subj-group><subject>Genome Sequencing</subject>
</subj-group>
</subj-group>
<subj-group><subject>Sequence Analysis</subject>
</subj-group>
</subj-group>
<subj-group><subject>Genomics</subject>
<subj-group><subject>Genome Analysis Tools</subject>
<subj-group><subject>Sequence Assembly Tools</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v2"><subject>Computer Science</subject>
<subj-group><subject>Computer Architecture</subject>
<subj-group><subject>Computer Hardware</subject>
</subj-group>
</subj-group>
<subj-group><subject>Computing Methods</subject>
</subj-group>
<subj-group><subject>Computing Systems</subject>
<subj-group><subject>Digital Computing</subject>
</subj-group>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title>ccTSA: A Coverage-Centric Threaded Sequence Assembler</article-title>
<alt-title alt-title-type="running-head">A Coverage-Centric Threaded Sequence Assembler</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Ahn</surname>
<given-names>Jung Ho</given-names>
</name>
<xref ref-type="aff" rid="aff1"></xref>
<xref ref-type="corresp" rid="cor1"><sup>*</sup>
</xref>
</contrib>
</contrib-group>
<aff id="aff1"><addr-line>Department of Intelligent Convergence Systems, Seoul National University, Seoul, Republic of Korea</addr-line>
</aff>
<contrib-group><contrib contrib-type="editor"><name><surname>Kingsford</surname>
<given-names>Carl</given-names>
</name>
<role>Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1">University of Maryland, United States of America</aff>
<author-notes><corresp id="cor1">* E-mail: <email>gajh@snu.ac.kr</email>
</corresp>
<fn fn-type="con"><p>Conceived and designed the experiments: JA. Performed the experiments: JA. Analyzed the data: JA. Contributed reagents/materials/analysis tools: JA. Wrote the paper: JA.</p>
</fn>
</author-notes>
<pub-date pub-type="collection"><year>2012</year>
</pub-date>
<pub-date pub-type="epub"><day>19</day>
<month>6</month>
<year>2012</year>
</pub-date>
<volume>7</volume>
<issue>6</issue>
<elocation-id>e39232</elocation-id>
<history><date date-type="received"><day>21</day>
<month>2</month>
<year>2012</year>
</date>
<date date-type="accepted"><day>21</day>
<month>5</month>
<year>2012</year>
</date>
</history>
<permissions><copyright-statement>Jung Ho Ahn.</copyright-statement>
<copyright-year>2012</copyright-year>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.</license-p>
</license>
</permissions>
<abstract><p>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.</p>
</abstract>
<counts><page-count count="13"></page-count>
</counts>
</article-meta>
</front>
</pmc>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Pmc/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001067 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Pmc/Curation/biblio.hfd -nk 001067 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= MersV1 |flux= Pmc |étape= Curation |type= RBID |clé= PMC:3378524 |texte= ccTSA: A Coverage-Centric Threaded Sequence Assembler }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Curation/RBID.i -Sk "pubmed:22723971" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Curation/biblio.hfd \ | NlmPubMed2Wicri -a MersV1
This area was generated with Dilib version V0.6.33. |