Exploiting sparseness in de novo genome assembly
Identifieur interne : 000951 ( Ncbi/Checkpoint ); précédent : 000950; suivant : 000952Exploiting 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.
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English descriptors
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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
Affiliations:
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PMC:3369186Le document en format XML
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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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<author><name sortKey="Zhang, L" uniqKey="Zhang L">L Zhang</name>
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<author><name sortKey="Schatz, Mc" uniqKey="Schatz M">MC Schatz</name>
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<author><name sortKey="Delcher, Al" uniqKey="Delcher A">AL Delcher</name>
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<author><name sortKey="Shen, Br" uniqKey="Shen B">BR Shen</name>
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<author><name sortKey="Phillippy, A" uniqKey="Phillippy A">A Phillippy</name>
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<author><name sortKey="Delcher, Al" uniqKey="Delcher A">AL Delcher</name>
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<author><name sortKey="Antonescu, C" uniqKey="Antonescu C">C Antonescu</name>
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<tree><noCountry><name sortKey="Ma, Zhanshan Sam" sort="Ma, Zhanshan Sam" uniqKey="Ma Z" first="Zhanshan Sam" last="Ma">Zhanshan Sam Ma</name>
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