CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing.
CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing.
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CLOVR：使用云计算从桌面上自动化和便携式序列分析的虚拟机。
DOI：
10.1186/1471-2105-12-356
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发表时间：
2011-08-30
影响因子：
3
通讯作者：
Fricke WF
中科院分区：
文献类型：
--
作者：
Angiuoli SV;Matalka M;Gussman A;Galens K;Vangala M;Riley DR;Arze C;White JR;White O;Fricke WF
下一代测序技术具有分散的序列采集，增加了对易于使用、跨多个平台便携且可扩展用于高通量应用的新生物信息学工具的需求。云计算平台通过互联网提供对计算基础设施的按需访问，并且可以与定制的虚拟机结合使用，以分发预先打包的预配置软件。我们描述了云虚拟资源，CloVR，一个新的桌面应用程序的按钮自动序列分析，可以利用云计算资源。CloVR作为一个便携式虚拟机（VM）实现，为微生物基因组学提供多个自动化分析管道，包括16S，全基因组和宏基因组序列分析。CloVR VM在个人计算机上运行，利用本地计算机资源，只需最少的安装，解决了部署生物信息学工作流程的关键挑战。此外，CloVR支持使用远程云计算资源来提高大规模序列处理的性能。在一个案例研究中，我们展示了使用CloVR在多个云计算平台上自动处理下一代测序数据。CloVR VM和相关架构降低了在本地单核和多核计算机以及云系统上利用复杂分析协议进行高吞吐量数据处理的门槛。
Next-generation sequencing technologies have decentralized sequence acquisition, increasing the demand for new bioinformatics tools that are easy to use, portable across multiple platforms, and scalable for high-throughput applications. Cloud computing platforms provide on-demand access to computing infrastructure over the Internet and can be used in combination with custom built virtual machines to distribute pre-packaged with pre-configured software. We describe the Cloud Virtual Resource, CloVR, a new desktop application for push-button automated sequence analysis that can utilize cloud computing resources. CloVR is implemented as a single portable virtual machine (VM) that provides several automated analysis pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis. The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. In addition CloVR supports use of remote cloud computing resources to improve performance for large-scale sequence processing. In a case study, we demonstrate the use of CloVR to automatically process next-generation sequencing data on multiple cloud computing platforms. The CloVR VM and associated architecture lowers the barrier of entry for utilizing complex analysis protocols on both local single- and multi-core computers and cloud systems for high throughput data processing.
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影响因子：
4.4
作者：
Aziz RK;Bartels D;Best AA;DeJongh M;Disz T;Edwards RA;Formsma K;Gerdes S;Glass EM;Kubal M;Meyer F;Olsen GJ;Olson R;Osterman AL;Overbeek RA;McNeil LK;Paarmann D;Paczian T;Parrello B;Pusch GD;Reich C;Stevens R;Vassieva O;Vonstein V;Wilke A;Zagnitko O
通讯作者：
Zagnitko O
影响因子：
14.9
作者：
Altschul, SF;Madden, TL;Lipman, DJ
通讯作者：
Lipman, DJ
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3
作者：
Afgan E;Baker D;Coraor N;Chapman B;Nekrutenko A;Taylor J
通讯作者：
Taylor J
影响因子：
5.6
作者：
ALTSCHUL, SF;GISH, W;LIPMAN, DJ
通讯作者：
LIPMAN, DJ
影响因子：
14.9
作者：
Punta M;Coggill PC;Eberhardt RY;Mistry J;Tate J;Boursnell C;Pang N;Forslund K;Ceric G;Clements J;Heger A;Holm L;Sonnhammer EL;Eddy SR;Bateman A;Finn RD
通讯作者：
Finn RD