The Velvet Assembler Using OpenACC Directives

E. B. Costa, Gabriel P. Silva
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引用次数: 0

Abstract

There are several programs available in bioinformatics for DNA sequence assembly. This is typically an extremely time-consuming endeavor, as DNA sequences can be extensive and intricate. Velvet was created to combine short and long read sequencing data into larger genomic sequences. Using OpenMP parallel programming, the last version of Velvet was created to support multiple threads. Through OpenACC directives, we present a new version of Velvet that takes advantage of multiprocessing using graphical processing units (GPU). Our tests demonstrate that this extension of Velvet allows for faster performance and efficient memory use.
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使用OpenACC指令的天鹅绒汇编器
有几个程序可用于DNA序列组装的生物信息学。这通常是一项极其耗时的工作,因为DNA序列可能是广泛而复杂的。创建Velvet是为了将短读和长读测序数据结合成更大的基因组序列。使用OpenMP并行编程,上一个版本的天鹅绒被创建为支持多线程。通过OpenACC指令,我们提出了一个利用图形处理单元(GPU)进行多处理的新版本的Velvet。我们的测试表明,这种对Velvet的扩展可以实现更快的性能和更高效的内存使用。
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