Exploiting sparseness in de novo genome assembly
Identifieur interne : 000942 ( Pmc/Curation ); précédent : 000941; suivant : 000943Exploiting sparseness in de novo genome assembly
Auteurs : Chengxi Ye [États-Unis] ; Zhanshan Sam Ma ; Charles H. Cannon [États-Unis] ; Mihai Pop [États-Unis] ; Douglas W. YuSource :
- BMC Bioinformatics [ 1471-2105 ] ; 2012.
Abstract
The very large memory requirements for the construction of assembly graphs for
In this paper, we demonstrate that constructing a sparse assembly graph which stores only a small fraction of the observed
We implement this sparse graph concept in a proof-of-principle software package,
Url:
DOI: 10.1186/1471-2105-13-S6-S1
PubMed: 22537038
PubMed Central: 3369186
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: Pour aller vers cette notice dans l'étape Curation :000942
Links to Exploration step
PMC:3369186Curation
No country items
Chengxi Ye<affiliation><nlm:aff id="I1">Ecology & Evolution of Plant-Animal Interaction Group, Xishuangbanna Tropical Botanic Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303 China</nlm:aff>
<wicri:noCountry code="subfield">Yunnan 666303 China</wicri:noCountry>
</affiliation>
<affiliation><nlm:aff id="I2">Ecology, Conservation, and Environment Center; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223 China</nlm:aff>
<wicri:noCountry code="subfield">Yunnan 650223 China</wicri:noCountry>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="I3">Department of Computer Science and Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Computer Science and Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD</wicri:regionArea>
</affiliation>
<affiliation><nlm:aff id="I2">Ecology, Conservation, and Environment Center; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223 China</nlm:aff>
<wicri:noCountry code="subfield">Yunnan 650223 China</wicri:noCountry>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="I3">Department of Computer Science and Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Computer Science and Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD</wicri:regionArea>
</affiliation>
<affiliation><nlm:aff id="I4">Computational Biology and Medical Ecology Lab; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223 China</nlm:aff>
<wicri:noCountry code="subfield">Yunnan 650223 China</wicri:noCountry>
</affiliation>
<affiliation><nlm:aff id="I5">Ecological Evolution Group, Xishuangbanna Tropical Botanic Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303 China</nlm:aff>
<wicri:noCountry code="subfield">Yunnan 666303 China</wicri:noCountry>
</affiliation>
<affiliation wicri:level="2"><nlm:aff id="I6">Department of Biological Sciences, Texas Tech University, Lubbock, TX 79410 USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Texas</region>
</placeName>
<wicri:cityArea>Department of Biological Sciences, Texas Tech University, Lubbock</wicri:cityArea>
</affiliation>
<affiliation><nlm:aff id="I2">Ecology, Conservation, and Environment Center; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223 China</nlm:aff>
<wicri:noCountry code="subfield">Yunnan 650223 China</wicri:noCountry>
</affiliation>
<affiliation><nlm:aff id="I7">School of Biological Sciences, University of East Anglia, Norwich, Norfolk NR47TJ UK</nlm:aff>
<wicri:noCountry code="subfield">Norfolk NR47TJ UK</wicri:noCountry>
</affiliation>
<affiliation><nlm:aff id="I7">School of Biological Sciences, University of East Anglia, Norwich, Norfolk NR47TJ UK</nlm:aff>
<wicri:noCountry code="subfield">Norfolk NR47TJ UK</wicri:noCountry>
</affiliation>
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Exploiting sparseness in <italic>de novo </italic>
genome assembly</title>
<author><name sortKey="Ye, Chengxi" sort="Ye, Chengxi" uniqKey="Ye C" first="Chengxi" last="Ye">Chengxi Ye</name>
<affiliation><nlm:aff id="I1">Ecology & Evolution of Plant-Animal Interaction Group, Xishuangbanna Tropical Botanic Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303 China</nlm:aff>
<wicri:noCountry code="subfield">Yunnan 666303 China</wicri:noCountry>
</affiliation>
<affiliation><nlm:aff id="I2">Ecology, Conservation, and Environment Center; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223 China</nlm:aff>
<wicri:noCountry code="subfield">Yunnan 650223 China</wicri:noCountry>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="I3">Department of Computer Science and Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Computer Science and Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Ma, Zhanshan Sam" sort="Ma, Zhanshan Sam" uniqKey="Ma Z" first="Zhanshan Sam" last="Ma">Zhanshan Sam Ma</name>
<affiliation><nlm:aff id="I4">Computational Biology and Medical Ecology Lab; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223 China</nlm:aff>
<wicri:noCountry code="subfield">Yunnan 650223 China</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Cannon, Charles H" sort="Cannon, Charles H" uniqKey="Cannon C" first="Charles H" last="Cannon">Charles H. Cannon</name>
<affiliation><nlm:aff id="I5">Ecological Evolution Group, Xishuangbanna Tropical Botanic Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303 China</nlm:aff>
<wicri:noCountry code="subfield">Yunnan 666303 China</wicri:noCountry>
</affiliation>
<affiliation wicri:level="2"><nlm:aff id="I6">Department of Biological Sciences, Texas Tech University, Lubbock, TX 79410 USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Texas</region>
</placeName>
<wicri:cityArea>Department of Biological Sciences, Texas Tech University, Lubbock</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Pop, Mihai" sort="Pop, Mihai" uniqKey="Pop M" first="Mihai" last="Pop">Mihai Pop</name>
<affiliation wicri:level="1"><nlm:aff id="I3">Department of Computer Science and Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Computer Science and Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Yu, Douglas W" sort="Yu, Douglas W" uniqKey="Yu D" first="Douglas W" last="Yu">Douglas W. Yu</name>
<affiliation><nlm:aff id="I2">Ecology, Conservation, and Environment Center; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223 China</nlm:aff>
<wicri:noCountry code="subfield">Yunnan 650223 China</wicri:noCountry>
</affiliation>
<affiliation><nlm:aff id="I7">School of Biological Sciences, University of East Anglia, Norwich, Norfolk NR47TJ UK</nlm:aff>
<wicri:noCountry code="subfield">Norfolk NR47TJ UK</wicri:noCountry>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">22537038</idno>
<idno type="pmc">3369186</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3369186</idno>
<idno type="RBID">PMC:3369186</idno>
<idno type="doi">10.1186/1471-2105-13-S6-S1</idno>
<date when="2012">2012</date>
<idno type="wicri:Area/Pmc/Corpus">000942</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000942</idno>
<idno type="wicri:Area/Pmc/Curation">000942</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000942</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Exploiting sparseness in <italic>de novo </italic>
genome assembly</title>
<author><name sortKey="Ye, Chengxi" sort="Ye, Chengxi" uniqKey="Ye C" first="Chengxi" last="Ye">Chengxi Ye</name>
<affiliation><nlm:aff id="I1">Ecology & Evolution of Plant-Animal Interaction Group, Xishuangbanna Tropical Botanic Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303 China</nlm:aff>
<wicri:noCountry code="subfield">Yunnan 666303 China</wicri:noCountry>
</affiliation>
<affiliation><nlm:aff id="I2">Ecology, Conservation, and Environment Center; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223 China</nlm:aff>
<wicri:noCountry code="subfield">Yunnan 650223 China</wicri:noCountry>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="I3">Department of Computer Science and Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Computer Science and Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Ma, Zhanshan Sam" sort="Ma, Zhanshan Sam" uniqKey="Ma Z" first="Zhanshan Sam" last="Ma">Zhanshan Sam Ma</name>
<affiliation><nlm:aff id="I4">Computational Biology and Medical Ecology Lab; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223 China</nlm:aff>
<wicri:noCountry code="subfield">Yunnan 650223 China</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Cannon, Charles H" sort="Cannon, Charles H" uniqKey="Cannon C" first="Charles H" last="Cannon">Charles H. Cannon</name>
<affiliation><nlm:aff id="I5">Ecological Evolution Group, Xishuangbanna Tropical Botanic Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303 China</nlm:aff>
<wicri:noCountry code="subfield">Yunnan 666303 China</wicri:noCountry>
</affiliation>
<affiliation wicri:level="2"><nlm:aff id="I6">Department of Biological Sciences, Texas Tech University, Lubbock, TX 79410 USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Texas</region>
</placeName>
<wicri:cityArea>Department of Biological Sciences, Texas Tech University, Lubbock</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Pop, Mihai" sort="Pop, Mihai" uniqKey="Pop M" first="Mihai" last="Pop">Mihai Pop</name>
<affiliation wicri:level="1"><nlm:aff id="I3">Department of Computer Science and Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Computer Science and Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Yu, Douglas W" sort="Yu, Douglas W" uniqKey="Yu D" first="Douglas W" last="Yu">Douglas W. Yu</name>
<affiliation><nlm:aff id="I2">Ecology, Conservation, and Environment Center; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223 China</nlm:aff>
<wicri:noCountry code="subfield">Yunnan 650223 China</wicri:noCountry>
</affiliation>
<affiliation><nlm:aff id="I7">School of Biological Sciences, University of East Anglia, Norwich, Norfolk NR47TJ UK</nlm:aff>
<wicri:noCountry code="subfield">Norfolk NR47TJ UK</wicri:noCountry>
</affiliation>
</author>
</analytic>
<series><title level="j">BMC Bioinformatics</title>
<idno type="eISSN">1471-2105</idno>
<imprint><date when="2012">2012</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>The very large memory requirements for the construction of assembly graphs for <italic>de novo </italic>
genome assembly limit current algorithms to super-computing environments.</p>
</sec>
<sec><title>Methods</title>
<p>In this paper, we demonstrate that constructing a sparse assembly graph which stores only a small fraction of the observed <italic>k-</italic>
mers as nodes and the links between these nodes allows the <italic>de novo </italic>
assembly of even moderately-sized genomes (~500 M) on a typical laptop computer.</p>
</sec>
<sec><title>Results</title>
<p>We implement this sparse graph concept in a proof-of-principle software package, <italic>SparseAssembler</italic>
, utilizing a new sparse <italic>k-</italic>
mer graph structure evolved from the <italic>de Bruijn </italic>
graph. We test our <italic>SparseAssembler </italic>
with both simulated and real data, achieving ~90% memory savings and retaining high assembly accuracy, without sacrificing speed in comparison to existing <italic>de novo </italic>
assemblers.</p>
</sec>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Pop, M" uniqKey="Pop M">M Pop</name>
</author>
<author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Myers, Ew" uniqKey="Myers E">EW Myers</name>
</author>
<author><name sortKey="Sutton, Gg" uniqKey="Sutton G">GG Sutton</name>
</author>
<author><name sortKey="Delcher, Al" uniqKey="Delcher A">AL Delcher</name>
</author>
<author><name sortKey="Dew, Im" uniqKey="Dew I">IM Dew</name>
</author>
<author><name sortKey="Fasulo, Dp" uniqKey="Fasulo D">DP Fasulo</name>
</author>
<author><name sortKey="Flanigan, Mj" uniqKey="Flanigan M">MJ Flanigan</name>
</author>
<author><name sortKey="Kravitz, Sa" uniqKey="Kravitz S">SA Kravitz</name>
</author>
<author><name sortKey="Mobarry, Cm" uniqKey="Mobarry C">CM Mobarry</name>
</author>
<author><name sortKey="Reinert, Khj" uniqKey="Reinert K">KHJ Reinert</name>
</author>
<author><name sortKey="Remington, Ka" uniqKey="Remington K">KA Remington</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Batzoglou, S" uniqKey="Batzoglou S">S Batzoglou</name>
</author>
<author><name sortKey="Jaffe, Db" uniqKey="Jaffe D">DB Jaffe</name>
</author>
<author><name sortKey="Stanley, K" uniqKey="Stanley K">K Stanley</name>
</author>
<author><name sortKey="Butler, J" uniqKey="Butler J">J Butler</name>
</author>
<author><name sortKey="Gnerre, S" uniqKey="Gnerre S">S Gnerre</name>
</author>
<author><name sortKey="Mauceli, E" uniqKey="Mauceli E">E Mauceli</name>
</author>
<author><name sortKey="Berger, B" uniqKey="Berger B">B Berger</name>
</author>
<author><name sortKey="Mesirov, Jp" uniqKey="Mesirov J">JP Mesirov</name>
</author>
<author><name sortKey="Lander, Es" uniqKey="Lander E">ES Lander</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mullikin, Jc" uniqKey="Mullikin J">JC Mullikin</name>
</author>
<author><name sortKey="Ning, Zm" uniqKey="Ning Z">ZM Ning</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Havlak, P" uniqKey="Havlak P">P Havlak</name>
</author>
<author><name sortKey="Chen, R" uniqKey="Chen R">R Chen</name>
</author>
<author><name sortKey="Durbin, Kj" uniqKey="Durbin K">KJ Durbin</name>
</author>
<author><name sortKey="Egan, A" uniqKey="Egan A">A Egan</name>
</author>
<author><name sortKey="Ren, Yr" uniqKey="Ren Y">YR Ren</name>
</author>
<author><name sortKey="Song, Xz" uniqKey="Song X">XZ Song</name>
</author>
<author><name sortKey="Weinstock, Gm" uniqKey="Weinstock G">GM Weinstock</name>
</author>
<author><name sortKey="Gibbs, Ra" uniqKey="Gibbs R">RA Gibbs</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Myers, Ew" uniqKey="Myers E">EW Myers</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Simpson, Jt" uniqKey="Simpson J">JT Simpson</name>
</author>
<author><name sortKey="Durbin, R" uniqKey="Durbin R">R Durbin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Birney, E" uniqKey="Birney E">E Birney</name>
</author>
<author><name sortKey="Zerbino, Dr" uniqKey="Zerbino D">DR Zerbino</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Birol, I" uniqKey="Birol I">I Birol</name>
</author>
<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, Sjm" uniqKey="Jones S">SJM Jones</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Chaisson, M" uniqKey="Chaisson M">M Chaisson</name>
</author>
<author><name sortKey="Pevzner, P" uniqKey="Pevzner P">P Pevzner</name>
</author>
<author><name sortKey="Tang, Hx" uniqKey="Tang H">HX Tang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gnerre, S" uniqKey="Gnerre S">S Gnerre</name>
</author>
<author><name sortKey="Maccallum, I" uniqKey="Maccallum I">I MacCallum</name>
</author>
<author><name sortKey="Przybylski, D" uniqKey="Przybylski D">D Przybylski</name>
</author>
<author><name sortKey="Ribeiro, Fj" uniqKey="Ribeiro F">FJ Ribeiro</name>
</author>
<author><name sortKey="Burton, Jn" uniqKey="Burton J">JN Burton</name>
</author>
<author><name sortKey="Walker, Bj" uniqKey="Walker B">BJ Walker</name>
</author>
<author><name sortKey="Sharpe, T" uniqKey="Sharpe T">T Sharpe</name>
</author>
<author><name sortKey="Hall, G" uniqKey="Hall G">G Hall</name>
</author>
<author><name sortKey="Shea, Tp" uniqKey="Shea T">TP Shea</name>
</author>
<author><name sortKey="Sykes, S" uniqKey="Sykes S">S Sykes</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Himmelbauer, H" uniqKey="Himmelbauer H">H Himmelbauer</name>
</author>
<author><name sortKey="Dohm, Jc" uniqKey="Dohm J">JC Dohm</name>
</author>
<author><name sortKey="Lottaz, C" uniqKey="Lottaz C">C Lottaz</name>
</author>
<author><name sortKey="Borodina, T" uniqKey="Borodina T">T Borodina</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Li, Rq" uniqKey="Li R">RQ Li</name>
</author>
<author><name sortKey="Zhu, Hm" uniqKey="Zhu H">HM Zhu</name>
</author>
<author><name sortKey="Ruan, J" uniqKey="Ruan J">J Ruan</name>
</author>
<author><name sortKey="Qian, Wb" uniqKey="Qian W">WB Qian</name>
</author>
<author><name sortKey="Fang, Xd" uniqKey="Fang X">XD Fang</name>
</author>
<author><name sortKey="Shi, Zb" uniqKey="Shi Z">ZB Shi</name>
</author>
<author><name sortKey="Li, Yr" uniqKey="Li Y">YR Li</name>
</author>
<author><name sortKey="Li, St" uniqKey="Li S">ST Li</name>
</author>
<author><name sortKey="Shan, G" uniqKey="Shan G">G Shan</name>
</author>
<author><name sortKey="Kristiansen, K" uniqKey="Kristiansen K">K Kristiansen</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Pevzner, Pa" uniqKey="Pevzner P">PA Pevzner</name>
</author>
<author><name sortKey="Tang, Hx" uniqKey="Tang H">HX Tang</name>
</author>
<author><name sortKey="Waterman, Ms" uniqKey="Waterman M">MS Waterman</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sundquist, A" uniqKey="Sundquist A">A Sundquist</name>
</author>
<author><name sortKey="Ronaghi, M" uniqKey="Ronaghi M">M Ronaghi</name>
</author>
<author><name sortKey="Tang, Hx" uniqKey="Tang H">HX Tang</name>
</author>
<author><name sortKey="Pevzner, P" uniqKey="Pevzner P">P Pevzner</name>
</author>
<author><name sortKey="Batzoglou, S" uniqKey="Batzoglou S">S Batzoglou</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Warren, Rl" uniqKey="Warren R">RL Warren</name>
</author>
<author><name sortKey="Sutton, Gg" uniqKey="Sutton G">GG Sutton</name>
</author>
<author><name sortKey="Jones, Sjm" uniqKey="Jones S">SJM Jones</name>
</author>
<author><name sortKey="Holt, Ra" uniqKey="Holt R">RA Holt</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Conway, Tc" uniqKey="Conway T">TC Conway</name>
</author>
<author><name sortKey="Bromage, Aj" uniqKey="Bromage A">AJ Bromage</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Marcais, G" uniqKey="Marcais G">G Marcais</name>
</author>
<author><name sortKey="Kingsford, C" uniqKey="Kingsford C">C Kingsford</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Melsted, P" uniqKey="Melsted P">P Melsted</name>
</author>
<author><name sortKey="Pritchard, Jk" uniqKey="Pritchard J">JK Pritchard</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Roberts, M" uniqKey="Roberts M">M Roberts</name>
</author>
<author><name sortKey="Hayes, W" uniqKey="Hayes W">W Hayes</name>
</author>
<author><name sortKey="Hunt, Br" uniqKey="Hunt B">BR Hunt</name>
</author>
<author><name sortKey="Mount, Sm" uniqKey="Mount S">SM Mount</name>
</author>
<author><name sortKey="Yorke, Ja" uniqKey="Yorke J">JA Yorke</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Deng, Hw" uniqKey="Deng H">HW Deng</name>
</author>
<author><name sortKey="Lin, Y" uniqKey="Lin Y">Y Lin</name>
</author>
<author><name sortKey="Li, J" uniqKey="Li J">J Li</name>
</author>
<author><name sortKey="Shen, H" uniqKey="Shen H">H Shen</name>
</author>
<author><name sortKey="Zhang, L" uniqKey="Zhang L">L Zhang</name>
</author>
<author><name sortKey="Papasian, Cj" uniqKey="Papasian C">CJ Papasian</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, Av" uniqKey="Zimin A">AV 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>
<author><name sortKey="Koren, S" uniqKey="Koren S">S Koren</name>
</author>
<author><name sortKey="Treangen, T" uniqKey="Treangen T">T Treangen</name>
</author>
<author><name sortKey="Schatz, Mc" uniqKey="Schatz M">MC Schatz</name>
</author>
<author><name sortKey="Delcher, Al" uniqKey="Delcher A">AL Delcher</name>
</author>
<author><name sortKey="Roberts, M" uniqKey="Roberts M">M Roberts</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhang, Wy" uniqKey="Zhang W">WY Zhang</name>
</author>
<author><name sortKey="Chen, Jj" uniqKey="Chen J">JJ Chen</name>
</author>
<author><name sortKey="Yang, Y" uniqKey="Yang Y">Y Yang</name>
</author>
<author><name sortKey="Tang, Yf" uniqKey="Tang Y">YF Tang</name>
</author>
<author><name sortKey="Shang, J" uniqKey="Shang J">J Shang</name>
</author>
<author><name sortKey="Shen, Br" uniqKey="Shen B">BR Shen</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mago, T" uniqKey="Mago T">T Magoč</name>
</author>
<author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name>
</author>
<author><name sortKey="Kurtz, S" uniqKey="Kurtz S">S Kurtz</name>
</author>
<author><name sortKey="Phillippy, A" uniqKey="Phillippy A">A Phillippy</name>
</author>
<author><name sortKey="Delcher, Al" uniqKey="Delcher A">AL Delcher</name>
</author>
<author><name sortKey="Smoot, M" uniqKey="Smoot M">M Smoot</name>
</author>
<author><name sortKey="Shumway, M" uniqKey="Shumway M">M Shumway</name>
</author>
<author><name sortKey="Antonescu, C" uniqKey="Antonescu C">C Antonescu</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Phillippy, Am" uniqKey="Phillippy A">AM Phillippy</name>
</author>
<author><name sortKey="Schatz, Mc" uniqKey="Schatz M">MC Schatz</name>
</author>
<author><name sortKey="Pop, M" uniqKey="Pop M">M Pop</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
<pmc article-type="research-article" xml:lang="en"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Bioinformatics</journal-id>
<journal-id journal-id-type="iso-abbrev">BMC Bioinformatics</journal-id>
<journal-title-group><journal-title>BMC Bioinformatics</journal-title>
</journal-title-group>
<issn pub-type="epub">1471-2105</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">22537038</article-id>
<article-id pub-id-type="pmc">3369186</article-id>
<article-id pub-id-type="publisher-id">1471-2105-13-S6-S1</article-id>
<article-id pub-id-type="doi">10.1186/1471-2105-13-S6-S1</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Proceedings</subject>
</subj-group>
</article-categories>
<title-group><article-title>Exploiting sparseness in <italic>de novo </italic>
genome assembly</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" corresp="yes" id="A1"><name><surname>Ye</surname>
<given-names>Chengxi</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I2">2</xref>
<xref ref-type="aff" rid="I3">3</xref>
<email>cxy@umd.edu</email>
</contrib>
<contrib contrib-type="author" id="A2"><name><surname>Ma</surname>
<given-names>Zhanshan Sam</given-names>
</name>
<xref ref-type="aff" rid="I4">4</xref>
<email>ma@vandals.uidaho.edu</email>
</contrib>
<contrib contrib-type="author" id="A3"><name><surname>Cannon</surname>
<given-names>Charles H</given-names>
</name>
<xref ref-type="aff" rid="I5">5</xref>
<xref ref-type="aff" rid="I6">6</xref>
<email>chuck@xtbg.ac.cn</email>
</contrib>
<contrib contrib-type="author" corresp="yes" id="A4"><name><surname>Pop</surname>
<given-names>Mihai</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
<email>mpop@umiacs.umd.edu</email>
</contrib>
<contrib contrib-type="author" corresp="yes" id="A5"><name><surname>Yu</surname>
<given-names>Douglas W</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<xref ref-type="aff" rid="I7">7</xref>
<email>douglas.yu@uea.ac.uk</email>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
Ecology & Evolution of Plant-Animal Interaction Group, Xishuangbanna Tropical Botanic Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303 China</aff>
<aff id="I2"><label>2</label>
Ecology, Conservation, and Environment Center; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223 China</aff>
<aff id="I3"><label>3</label>
Department of Computer Science and Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA</aff>
<aff id="I4"><label>4</label>
Computational Biology and Medical Ecology Lab; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223 China</aff>
<aff id="I5"><label>5</label>
Ecological Evolution Group, Xishuangbanna Tropical Botanic Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303 China</aff>
<aff id="I6"><label>6</label>
Department of Biological Sciences, Texas Tech University, Lubbock, TX 79410 USA</aff>
<aff id="I7"><label>7</label>
School of Biological Sciences, University of East Anglia, Norwich, Norfolk NR47TJ UK</aff>
<pub-date pub-type="collection"><year>2012</year>
</pub-date>
<pub-date pub-type="epub"><day>19</day>
<month>4</month>
<year>2012</year>
</pub-date>
<volume>13</volume>
<issue>Suppl 6</issue>
<supplement><named-content content-type="supplement-title">Proceedings of the Second Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-seq 2012)</named-content>
<named-content content-type="supplement-editor">Paul Medvedev and Eleazar Eskin</named-content>
</supplement>
<fpage>S1</fpage>
<lpage>S1</lpage>
<permissions><copyright-statement>Copyright ©2012 Ye et al.; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2012</copyright-year>
<copyright-holder>Ye et al.; licensee BioMed Central Ltd.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-p>This is an open access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<self-uri xlink:href="http://www.biomedcentral.com/1471-2105/13/S6/S1"></self-uri>
<abstract><sec><title>Background</title>
<p>The very large memory requirements for the construction of assembly graphs for <italic>de novo </italic>
genome assembly limit current algorithms to super-computing environments.</p>
</sec>
<sec><title>Methods</title>
<p>In this paper, we demonstrate that constructing a sparse assembly graph which stores only a small fraction of the observed <italic>k-</italic>
mers as nodes and the links between these nodes allows the <italic>de novo </italic>
assembly of even moderately-sized genomes (~500 M) on a typical laptop computer.</p>
</sec>
<sec><title>Results</title>
<p>We implement this sparse graph concept in a proof-of-principle software package, <italic>SparseAssembler</italic>
, utilizing a new sparse <italic>k-</italic>
mer graph structure evolved from the <italic>de Bruijn </italic>
graph. We test our <italic>SparseAssembler </italic>
with both simulated and real data, achieving ~90% memory savings and retaining high assembly accuracy, without sacrificing speed in comparison to existing <italic>de novo </italic>
assemblers.</p>
</sec>
</abstract>
<conference><conf-date>19-20 April 2012</conf-date>
<conf-name>Second Annual RECOMB Satellite Workshop on Massively Parallel Sequencing</conf-name>
<conf-loc>Barcelona, Spain</conf-loc>
</conference>
</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 000942 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Pmc/Curation/biblio.hfd -nk 000942 | 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:3369186 |texte= Exploiting sparseness in de novo genome assembly }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Curation/RBID.i -Sk "pubmed:22537038" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Curation/biblio.hfd \ | NlmPubMed2Wicri -a MersV1
This area was generated with Dilib version V0.6.33. |