WHOLE GENOME ASSEMBLY FROM NEXTGEN SEQUENCING SHORT READ DATA

这个子项目是许多利用资源的研究子项目之一 由NIH/NCRR资助的中心拨款提供。子项目的主要支持 而子项目的主要调查员可能是由其他来源提供的， 包括其它NIH来源。 列出的子项目总成本可能 代表子项目使用的中心基础设施的估计数量， 而不是由NCRR赠款提供给子项目或子项目工作人员的直接资金。 请求：30，000个SU和12个月的高级用户支持摘要：这个启动项目将探索如何最好地利用匹兹堡超级计算中心的Blacklight进行下一代测序数据和基因组分析应用。将安装以下软件系统，并选择适当的组件，测试和基准测试，以使TeraGrid研究提案的发展：（1）应用生物系统生物显微镜包。(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支持该项目。下面我们提供这两个包的更多背景。AB Bioscope -此软件包在Blacklight上的友好用户期间成功安装并运行。有一些效率问题，这将在1月初黑光进入生产时得到解决。CLC生物基因组学软件/服务器-CLC软件分为服务器和客户端。从用户的角度来看，两者都有基本相同的分析工具，但服务器允许客户机一次启动多个作业（而客户机通常一次只能启动单个作业）。服务器是我们在实验室里运行的。CLC Genomics服务器可以一次对多个作业进行排队，并且通过连接多个节点，可以并行处理作业。“客户端”工作台是图形化的、向导驱动的工具，对于生物学家来说运行起来相对简单。它可以在X-Windows中运行。客户端作为非常强大的桌面解决方案，但也可以是“客户端”，当你有机会访问CLC生物服务器解决方案。CLC Bio Assembly Cell -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，然后将其迁移到CLC Genomics产品和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Blacklight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，用于我们对Blacklight的测试。高级用户支持在友好用户期间，我们与PSC的Jana和Sanielevici博士合作。他们对我们工作的持续支持在这个启动项目中非常重要。

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.