WHOLE GENOME ASSEMBLY FROM NEXTGEN SEQUENCING SHORT READ DATA

来自下一代测序短读数据的全基因组组装

• 批准号: 8364347
• 负责人: CECILIA W. LO
• 金额: $ 0.11万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-15 至 2013-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8364347
• 关键词: Address; Algorithms; Benchmarking; Biomedical Research; CLC Gene; Client; Computer software; Data; Development; Funding; Genome; Genomics; Grant; High Performance Computing; Licensing; Modeling; National Center for Research Resources; Occupations; Principal Investigator; Production; Reading; Research; Research Infrastructure; Research Proposals; Research Support; Resources; Running; Solutions; Source; Supercomputing; Testing; Time; United States National Institutes of Health; Work; abstracting; analytical tool; cell assembly; cost; next generation; parallel processing; software systems; tool; user-friendly

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Request: 30,000 SUs and 12 months Advanced User Support Abstract: This startup project will explore how best to leverage Blacklight at the Pittsburgh Supercomputing Center for next-generation sequencing data and genome analysis applications. The following software systems will be installed, and appropriate components selected, tested and benchmarked to enable the development of a TeraGrid research proposal: (1) Applied Biosystems Bioscope package. (2) CLC Bio software. Both ABI and CLC will support this project with trial licenses and developer expertise. Below we provide additional background on these two packages. AB Bioscope - This package was installed and run successfully during the friendly user period on Blacklight. There were some efficiency issues, which will be addressed when Blacklight enters production in early January. CLC Bio Genomics Workbench / server -The CLC software is split into a server and clients. Both have essentially identical analytical tools from the user perspective, but the server allows clients to initiate multiple jobs at once (whereas the clients are limited to single jobs at a time, typically). The server is what we run in our lab. The CLC Genomics server can queue multiple jobs at once, and with multiple nodes attached, can parallel process jobs. The "client" Workbenches are graphical, wizard driven tools that are relatively simple for biologists to run. This can run in X-windows. The clients function as very capable desktop solutions, but can also be the "client" when you have access to the CLC Bio server solution. CLC Bio Assembly Cell - This is the CLC Bio command line product, where CLC Bio first implements new development in these algorithms after which they get migrated to both the CLC Genomics Workbench, and the Genomics Server products. We plan to focus on this first, and see how it could support research that could only be done on Blacklight. Then we will investigate how Blacklight can fit into the Client-Server model. We have obtained a trial license for this product, for our tests on Blacklight. Advanced User Support During the friendly user period we have worked with Drs. Jana and Sanielevici at PSC. Their continued support of our work will be very important during this startup project.

该副本是利用资源的众多研究子项目之一 由NIH/NCRR资助的中心赠款提供。对该子弹的主要支持 而且，副投影的主要研究员可能是其他来源提供的 包括其他NIH来源。 列出的总费用可能 代表subproject使用的中心基础架构的估计量， NCRR赠款不直接向子弹或副本人员提供的直接资金。 请求：30,000 sus和12个月的高级用户支持摘要：该启动项目将探讨如何最好地利用匹兹堡超级计算中心的黑光进行下一代测序数据和基因组分析应用程序。将安装以下软件系统，并通过选择，测试和基准选择适当的组件，以实现TeraGRID研究建议的开发：（1）Applied Biosystems Bioscope软件包。 （2）CLC BIO软件。 ABI和CLC都将通过试用许可证和开发人员专业知识来支持该项目。在下面，我们提供了这两个软件包的其他背景。 AB Bioscope-安装了此软件包，并在Blacklight上的友好用户期间成功运行。有一些效率问题，当黑人在1月初进入生产时，将解决这些问题。 CLC Bio Genomics Workbench /服务器 - CLC软件分为服务器和客户端。从用户角度来看，两者都具有基本相同的分析工具，但是服务器允许客户端一次启动多个作业（而客户端通常一次仅限于单个作业（通常是一次）。服务器是我们在实验室中运行的服务。 CLC基因组学服务器可以一次排队多个作业，并且随附多个节点可以并行处理作业。 “客户端”工作台是图形的，向导驱动的工具，对于生物学家来说相对简单。这可以在X-Windows中运行。客户端可以用作功能强大的桌面解决方案，但是当您可以访问CLC Bio Server解决方案时，也可以成为“客户端”。 CLC BIO组装单元格 - 这是CLC Bio命令行产品，CLC Bio首先在这些算法中实现新的开发，然后它们迁移到CLC Genomics Workbench和Genomics Server产品。我们计划首先关注这一点，看看它如何支持只能在黑光上进行的研究。然后，我们将研究黑光如何适应客户端服务器模型。我们已经获得了该产品的试用许可证，用于黑光测试。在友好的用户期间，我们与DRS合作的高级用户支持。 Jana和Sanielevici在PSC。他们对我们的工作的持续支持将非常重要。