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GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads

Andrea Manconi, Alessandro Orro, Emanuele Manca, Giuliano Armano, Luciano Milanesi
Institute for Biomedical Technologies, National Research Council, Segrate (Mi), Italy
PLoS ONE 9(5): e97277, 2014

@article{manconi2014gpu,

   title={GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads},

   author={Manconi, Andrea and Orro, Alessandro and Manca, Emanuele and Armano, Giuliano and Milanesi, Luciano},

   journal={PLOS ONE},

   volume={9},

   number={5},

   pages={e97277},

   year={2014},

   publisher={Public Library of Science}

}

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Cytosine DNA methylation is an epigenetic mark implicated in several biological processes. Bisulfite treatment of DNA is acknowledged as the gold standard technique to study methylation. This technique introduces changes in the genomic DNA by converting cytosines to uracils while 5-methylcytosines remain nonreactive. During PCR amplification 5-methylcytosines are amplified as cytosine, whereas uracils and thymines as thymine. To detect the methylation levels, reads treated with the bisulfite must be aligned against a reference genome. Mapping these reads to a reference genome represents a significant computational challenge mainly due to the increased search space and the loss of information introduced by the treatment. To deal with this computational challenge we devised GPU-BSM, a tool based on modern Graphics Processing Units. Graphics Processing Units are hardware accelerators that are increasingly being used successfully to accelerate general-purpose scientific applications. GPU-BSM is a tool able to map bisulfite-treated reads from whole genome bisulfite sequencing and reduced representation bisulfite sequencing, and to estimate methylation levels, with the goal of detecting methylation. Due to the massive parallelization obtained by exploiting graphics cards, GPU-BSM aligns bisulfite-treated reads faster than other cutting-edge solutions, while outperforming most of them in terms of unique mapped reads.
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