Continued improvement of genome assemblies and assembly techniques for Next Gener

描述（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，以最低的成本产生最佳的组装。我们建议继续开发我们的软件，以关闭差距和固定错误的组装我们的拍摄方法。我们可以扩展该方法，使用额外的NGS读取和配对对来关闭现有装配中的间隙，以增加相邻性，并发现和纠正错误装配。这种方法可以作为传统整理技术的廉价替代品。任何组装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，能够利用配偶对和标记数据从组装的组群中产生染色体序列。我们的初步版本适用于具有大型contigs的程序集（N50大小>100Kb）。由NGS数据组装的基因组通常具有较小的contigs （N50大小为10-20Kb）。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上一个项目期间获得的经验，从现有的Trace Archive数据结合（如果有的话）额外的NGS数据，重新组装鸡、大鼠和可能对公共卫生有兴趣的其他基因组。NGS的数据越来越便宜了。现在有很多研究小组对各种基因组测序感兴趣。因此，我们建议与产生数据的中心合作，重新组装昆虫、植物基因组和其他对公共卫生有兴趣的生物体。我们的目标是作为一个专家基因组组装组，为社会提供服务和技术。

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.