GAMS: Genome Assembly on Multi-GPU Using String Graph
GAMS: Genome Assembly on Multi-GPU Using String Graph
复制标题
GAMS：使用字符串图在多 GPU 上进行基因组组装
DOI：
10.1109/hpcc-smartcity-dss.2016.0057
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发表时间：
2016
期刊：
影响因子：
--
通讯作者：
K. Paul
中科院分区：
文献类型：
--
作者：
Gaurav Jain;Lalchand Rathore;K. Paul
基因组序列拼接是生物信息学中计算密集型的问题。已经提出了许多并行算法来加速多核以及机器集群。近年来，GPU的计算能力的提高使得来自各个研究领域的应用能够利用GPU中可用的大量“核”以及并行地一起工作的多个GPU。在本文中，我们提出了一个多GPU为基础的序列组装使用Nvidia的GPU的设计和开发。我们使用字符串图的方法来规避有限的内存在GPU中建立一个并行的解决方案，字符串图是一个内存有效的数据结构。我们的汇编器（GAMS）采用当前NGS技术产生的fasta格式的读取文件来构建字符串图。重叠群是通过将图中可以明确连接的区域分组而形成的。在本文中，我们还提出了并行算法的字符串图的建设和图形简化。我们已经将我们的汇编程序基准化到了5个细菌基因组和人类基因组的chr 22上。我们的研究结果表明，多GPU上的设计提供了一个6- 7倍的加速比最先进的并行天鹅绒实现。生产的组件质量也明显更好。
Genome Sequence assembly is a very compute intensive problem in the field of bio-informatics. Many parallel algorithms has been proposed to accelerate this on multicores as well as clusters of machines. In recent times, the improved computation power of GPUs has enabled applications from various research fields to take advantage of the massive number of "cores" available in GPUs and multiple GPUs working together in parallel. In this paper we present the design and development of a Multi-GPU based assembler for sequence assembly using Nvidia's GPUs. We use the String Graph approach to circumvent the limited memory available in GPUs to build a parallel solution given that the string graph is a memory efficient data structure. Our assembler (GAMS) takes in a file of reads in fasta format produced by the current NGS technologies to build the string graph. Contigs are formed by grouping the regions of graph which can be unambiguously connected. In this paper, we also present parallel algorithms for string graph construction and graph simplification. We have benchmarked our assembler on five bacterial genomes and chr22 of the human genome. Our results show that the design on the Multi-GPU provides a 6-7x speedup over a state of the art parallel Velvet implementation. The quality of assembly produced is also significantly better.
影响因子：
7
作者：
Huang, XQ;Wang, JM;Hillier, L
通讯作者：
Hillier, L