Continued improvement of genome assemblies and assembly techniques for Next Gener

描述（由申请人提供）：两种广泛使用的下一代测序（NGS）技术是454测序和Illumina测序。我们建议确定最佳测序策略，即454和Illumina读取和配对数据的最佳组合，以最低成本产生最佳可能的组装。我们建议继续开发我们的软件，通过我们的拍摄方法来缩小差距和修复错误装配。我们可以扩展该方法以使用额外的NGS读段和配偶对来闭合现有组装中的缺口以增加邻接性，并发现和纠正错误组装。这种方法可以作为传统整理技术的廉价替代品。任何装配项目的最终产品都是一组染色体序列文件。我们建议开发改进的软件，能够使用配偶对和标记数据从组装的重叠群产生染色体序列。我们的初步版本适用于具有大重叠群（N50大小> 100 Kb）的组件。从NGS数据组装的基因组通常具有小的重叠群（N50大小为10- 20 Kb）。我们建议扩展软件的开发，使其适用于NGS数据的基因组组装。我们建议利用我们在前一个项目期间获得的经验，从现有的Trace Archive数据中结合（如果可用）额外的NGS数据，重新组装鸡，大鼠和其他可能具有公共卫生利益的基因组。NGS数据变得越来越便宜。现在有许多团体对各种基因组的测序感兴趣。因此，我们建议与产生数据的中心合作，重新组装昆虫、植物基因组和其他公共卫生感兴趣的生物。我们的目标是作为一个专家基因组组装小组，为社区提供服务和技术。 公共卫生相关性：与桑格测序相比，测序技术的进步使得以低成本快速获得大量序列数据成为可能。我们的目标是将我们的技术、软件和专业知识贡献给社区。我们将不断改进我们的方法，以获得最好的组装新的基因组测序与最新的技术。该项目的最终目标是通过更好地了解人类基因组和其他物种的基因组来改善公共卫生。

DESCRIPTION (provided by applicant): The two widely used Next Generation Sequencing (NGS) technologies are 454 Sequencing and Illumina sequencing. We propose to determine the best sequencing strategy, that is the optimal mix of 454 and Illumina read and mate pair data to produce the best possible assembly at the lowest cost. We propose to continue developing our software for closing gaps and fixing mis- assemblies by our shooting method. We can extend the method to use additional NGS reads and mate pairs to close gaps in existing assemblies to increase contiguity, and find and correct mis-assemblies. This method can be used as a cheaper alternative to traditional finishing techniques. The final product of any assembly project is a set of the chromosome sequence files. We propose to develop improved software capable of producing chromosome sequences from the assembled contigs using mate pair and marker data. Our preliminary version works for assemblies that have large contigs (N50 size >100Kb). Genomes assembled from the NGS data typically have small contigs (N50 size of 10-20Kb). We propose to extend development of the software so that it is applicable to genome assemblies of the NGS data. We propose to employ the experience that we gained in the previous project period to re-assemble the genomes of chicken, rat, and possibly other genomes of public health interest from the existing Trace Archive data combined with (if available) additional NGS data. The NGS data is getting cheaper. Now there are many groups interested in sequencing various genomes. Thus we propose to produce de novo assemblies of insect, plant genomes and other organisms of public health interest in collaboration with the centers that generate the data. Our goal is to serve as an expert genome assembly group that provides its services and techniques to the community. PUBLIC HEALTH RELEVANCE: Advances in the sequencing technologies made it possible to obtain large amounts of sequence data quickly and at low cost, compared to the Sanger sequencing. Our goals are to contribute our techniques, software and expertise in assembly of the short read data to the community. We will continuously improve our methods to obtain the best possible assemblies of the new genomes sequenced with the latest technologies. The ultimate goal of this project is to improve public health by better understanding the human genome and the genomes of other species.