%0 Journal Article %J BMC bioinformatics %D 2012 %T Exploiting sparseness in de novo genome assembly %A Ye, C. %A Ma, Z.S. %A Cannon, C.H. %A Pop, Mihai %A Yu, D.W. %X The very large memory requirements for the construction of assembly graphs for de novo genome assembly limit current algorithms to super-computing environments.In this paper, we demonstrate that constructing a sparse assembly graph which stores only a small fraction of the observed k-mers as nodes and the links between these nodes allows the de novo assembly of even moderately-sized genomes (~500 M) on a typical laptop computer. We implement this sparse graph concept in a proof-of-principle software package, SparseAssembler, utilizing a new sparse k-mer graph structure evolved from the de Bruijn graph. We test our SparseAssembler with both simulated and real data, achieving ~90% memory savings and retaining high assembly accuracy, without sacrificing speed in comparison to existing de novo assemblers. %B BMC bioinformatics %V 13 %8 2012 %G eng %N Suppl 6