Exploiting sparseness in de novo genome assembly
Title | Exploiting sparseness in de novo genome assembly |
Publication Type | Journal Articles |
Year of Publication | 2012 |
Authors | Ye C, Ma ZS, Cannon CH, Pop M, Yu DW |
Journal | BMC bioinformatics |
Volume | 13 |
Issue | Suppl 6 |
Date Published | 2012 |
Abstract | 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. |