孟德尔 GPU：图形处理单元上的单倍型分型和基因型推断。
Mendel-GPU: haplotyping and genotype imputation on graphics processing units.
机构信息
Department of Preventive Medicine, USC, Los Angeles, CA 90089, USA.
出版信息
Bioinformatics. 2012 Nov 15;28(22):2979-80. doi: 10.1093/bioinformatics/bts536. Epub 2012 Sep 5.
Abstract
MOTIVATION
In modern sequencing studies, one can improve the confidence of genotype calls by phasing haplotypes using information from an external reference panel of fully typed unrelated individuals. However, the computational demands are so high that they prohibit researchers with limited computational resources from haplotyping large-scale sequence data.
RESULTS
Our graphics processing unit based software delivers haplotyping and imputation accuracies comparable to competing programs at a fraction of the computational cost and peak memory demand.
AVAILABILITY
Mendel-GPU, our OpenCL software, runs on Linux platforms and is portable across AMD and nVidia GPUs. Users can download both code and documentation at http://code.google.com/p/mendel-gpu/.
CONTACT
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
动机
在现代测序研究中，可以通过使用来自完全分型无关个体的外部参考面板的信息来对单倍型进行相位，从而提高基因型调用的置信度。然而，计算需求如此之高，以至于限制了计算资源有限的研究人员对大规模序列数据进行单倍型分析。
结果
我们基于图形处理单元的软件以计算成本和峰值内存需求的一小部分提供了与竞争程序相当的单倍型分析和插补准确性。
可用性
Mendel-GPU 是我们的 OpenCL 软件，可在 Linux 平台上运行，并且可在 AMD 和 nVidia GPU 之间移植。用户可以在 http://code.google.com/p/mendel-gpu/ 下载代码和文档。
联系人
补充信息
补充数据可在 Bioinformatics 在线获得。
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