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。454平台等下一代DNA测序仪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复杂的组装软件将一组读数转换为染色体长度的序列。赛莱拉装配机是一家领先的装配机，在基因组学领域保持了10年的领先地位。它使桑格化学公司对真核生物基因组和元基因组样本进行测序的突破性出版物成为可能。现在，Celera汇编器也支持454技术。Celera汇编器是在构建重叠群和从454个读取和配对数据集进行重复解析方面最积极的软件。Celera汇编器是处理人类基因组规模项目中涉及的大型数据集的唯一汇编器。新的资金将使几个重要的算法扩展成为可能。该软件将在Sanger、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。它将获得结合参考序列的能力，作为从头组装的辅助。它的数据模型将得到改进，以提高对真实数据的精度。该软件将能够整合通过定向测序或其他方式产生的非猎枪读数。它将加强环境样品的元基因组学组装。软件工程的改进将有助于算法的开发。为了能够更广泛地采用Celera汇编程序，该项目将包括文件编制、培训、终端用户支持以及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.