The Velvet Assembler Using OpenACC Directives

E. B. Costa, Gabriel P. Silva
{"title":"The Velvet Assembler Using OpenACC Directives","authors":"E. B. Costa, Gabriel P. Silva","doi":"10.29007/pzbt","DOIUrl":null,"url":null,"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.","PeriodicalId":93549,"journal":{"name":"EPiC series in computing","volume":"1 1","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"EPiC series in computing","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.29007/pzbt","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
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.
查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
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。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 去求助
来源期刊
CiteScore
1.60
自引率
0.00%
发文量
0
期刊最新文献
ARCH-COMP23 Category Report: Hybrid Systems Theorem Proving ARCH-COMP23 Category Report: Continuous and Hybrid Systems with Linear Continuous Dynamics ARCH-COMP23 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics ARCH-COMP23 Repeatability Evaluation Report ARCH-COMP23 Category Report: Artificial Intelligence and Neural Network Control Systems (AINNCS) for Continuous and Hybrid Systems Plants
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1