Continued Development of the Celera Whole Genome Shotgun Assembler

描述（由申请人提供）：摘要DNA测序使生物医学发现成为可能。下一代DNA测序仪，如454平台，为传统的桑格测序提供了具有成本效益的替代方案。所有测序平台都依赖于复杂的组装软件来将读取的集合转化为染色体长度的序列。Celera Assembler是一家领先的组装公司，10年来一直处于基因组学的最前沿。它使突破性的出版物的真核基因组和宏基因组样品测序的桑格化学。现在，Celera Assembler也支持454技术。Celera Assembler是在从454个读段和配偶对数据集构建重叠群和解析重复序列方面最积极的软件。Celera Assembler是唯一一个处理人类基因组规模项目中涉及的大型数据集的汇编程序。新的资金将使几个重要的算法扩展。该软件将在桑格、454和混合数据集上显示改进的性能和产量。该软件将获得在组装较长读取期间利用短读取下一代数据的能力。它将获得并入参考序列作为从头组装辅助的能力。将改进其数据模型，以提高对真实的数据的精确度。该软件将能够整合通过定向测序或其他手段生成的非鸟枪法读数。它将增强环境样品的宏基因组学组装。软件工程的改进将有助于算法的开发。为了使Celera汇编程序得到更广泛的采用，该项目将包括文档、培训、最终用户支持以及对与数据源和分析工具集成的支持。

DESCRIPTION (provided by applicant): Abstract DNA sequencing enables biomedical discovery. Next-generation DNA sequencers such as the 454 platform provide cost-effective alternatives to traditional Sanger sequencing. All sequencing platforms rely on sophisticated assembly software to transform a collection of reads into chromosome-length sequences. Celera Assembler is a premier assembler that has remained at the forefront of genomics for 10 years. It has enabled ground-breaking publications of eukaryotic genomes and metagenomic samples sequenced by Sanger chemistry. Now, the Celera Assembler also supports the 454 technology. Celera Assembler is the software most aggressive at contig construction and repeat resolution from 454 read and mate pair data sets. Celera Assembler is the only assembler that handles the large data sets involved in human-genome-scale projects. Renewed funding will enable several important algorithms extensions. The software will show improved performance and yield on Sanger, 454, and hybrid data sets. The software will gain capability to exploit short-read next-generation data during assembly of longer reads. It will gain the ability to incorporate reference sequences as an assist to de novo assembly. Its data model will be refined for increased precision on real data. The software will be able to integrate non-shotgun reads generated by directed sequencing or other means. It will enhance metagenomics assembly of environmental samples. Software engineering improvements will assist the algorithms development. To enable the wider adoption of the Celera Assembler, the project will include documentation, training, end-user support, and support for integration with data sources and analysis tools.