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
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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>
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<affiliation><nlm:aff id="I7">School of Biological Sciences, University of East Anglia, Norwich, Norfolk NR47TJ UK</nlm:aff>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Exploiting sparseness in <italic>de novo </italic>
genome assembly</title>
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<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>
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<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>
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