ccTSA: A Coverage-Centric Threaded Sequence Assembler
Identifieur interne : 002198 ( Main/Curation ); précédent : 002197; suivant : 002199ccTSA: A Coverage-Centric Threaded Sequence Assembler
Auteurs : Jung Ho AhnSource :
- PLoS ONE [ 1932-6203 ] ; 2012.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- methods : Computational Biology, Sequence Analysis.
- Algorithms, Animals, Genome, Humans, Internet, Software.
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
- to stream Pmc, to step Curation: Pour aller vers cette notice dans l'étape Curation :001067
- to stream Pmc, to step Checkpoint: Pour aller vers cette notice dans l'étape Curation :001279
- to stream PubMed, to step Corpus: Pour aller vers cette notice dans l'étape Curation :001D71
- to stream PubMed, to step Curation: Pour aller vers cette notice dans l'étape Curation :001D71
- to stream PubMed, to step Checkpoint: Pour aller vers cette notice dans l'étape Curation :001C23
- to stream Ncbi, to step Merge: Pour aller vers cette notice dans l'étape Curation :000972
- to stream Ncbi, to step Curation: Pour aller vers cette notice dans l'étape Curation :000972
- to stream Ncbi, to step Checkpoint: Pour aller vers cette notice dans l'étape Curation :000972
- to stream Main, to step Merge: Pour aller vers cette notice dans l'étape Curation :002223
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>
<idno type="wicri:Area/Pmc/Checkpoint">001279</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001279</idno>
<idno type="wicri:source">PubMed</idno>
<idno type="RBID">pubmed:22723971</idno>
<idno type="wicri:Area/PubMed/Corpus">001D71</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001D71</idno>
<idno type="wicri:Area/PubMed/Curation">001D71</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001D71</idno>
<idno type="wicri:Area/PubMed/Checkpoint">001C23</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001C23</idno>
<idno type="wicri:Area/Ncbi/Merge">000972</idno>
<idno type="wicri:Area/Ncbi/Curation">000972</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">000972</idno>
<idno type="wicri:Area/Main/Merge">002223</idno>
<idno type="wicri:Area/Main/Curation">002198</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><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term>
<term>Animals</term>
<term>Computational Biology (methods)</term>
<term>Genome</term>
<term>Humans</term>
<term>Internet</term>
<term>Sequence Analysis (methods)</term>
<term>Software</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term>
<term>Analyse de séquence ()</term>
<term>Animaux</term>
<term>Biologie informatique ()</term>
<term>Génome</term>
<term>Humains</term>
<term>Internet</term>
<term>Logiciel</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term>
<term>Sequence Analysis</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Algorithms</term>
<term>Animals</term>
<term>Genome</term>
<term>Humans</term>
<term>Internet</term>
<term>Software</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term>
<term>Analyse de séquence</term>
<term>Animaux</term>
<term>Biologie informatique</term>
<term>Génome</term>
<term>Humains</term>
<term>Internet</term>
<term>Logiciel</term>
</keywords>
</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>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002198 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Curation/biblio.hfd -nk 002198 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= MersV1 |flux= Main |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/Main/Curation/RBID.i -Sk "pubmed:22723971" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Curation/biblio.hfd \ | NlmPubMed2Wicri -a MersV1
This area was generated with Dilib version V0.6.33. |