Continued Development of the Celera Whole Genome Shotgun Assembler

Celera 全基因组霰弹枪组装机的持续开发

• 批准号: 7916754
• 负责人: Jason Rafe Miller
• 金额: $ 59.86万
• 依托单位: J. CRAIG VENTER INSTITUTE, INC.
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-05-11 至 2012-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7916754
• 关键词: Address; Adoption; Algorithms; Biology; Characteristics; Chemistry; Chromosomes; Collection; Communities; Computer software; DNA; DNA Sequence; Data; Data Set; Data Sources; Development; Dideoxy Chain Termination DNA Sequencing; Documentation; Ecosystem; Engineering; Funding; Genes; Genome; Genomics; Goals; Human Genome; Hybrids; Individual; Length; Maintenance; Metagenomics; Partner in relationship; Pathway interactions; Performance; Publications; Publishing; Reading; Reporting; Research; Research Infrastructure; Resolution; Running; Sampling; Scientist; Shotguns; Site; Software Engineering; Source; Source Code; System; Technology; Testing; Time; Training; Trees; abstracting; base; cost; data modeling; forging; improved; interoperability; next generation; novel; open source; public health research; tool; web site

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.

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 Sanger 测序提供了经济高效的替代方案。所有测序平台都依赖复杂的组装软件将读数集合转换为染色体长度的序列。 Celera Assembler 是一款一流的汇编器，10 年来一直处于基因组学的前沿。它使得通过桑格化学测序的真核基因组和宏基因组样本的突破性发表成为可能。现在，Celera Assembler 也支持 454 技术。 Celera Assembler 是在 454 个读取和配对数据集的重叠群构建和重复解析方面最积极的软件。 Celera Assembler 是唯一能够处理人类基因组规模项目中涉及的大型数据集的汇编器。更新的资金将实现几个重要的算法扩展。该软件将在 Sanger、454 和混合数据集上显示出改进的性能和产量。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。它将获得合并参考序列的能力，以协助从头组装。其数据模型将得到改进，以提高真实数据的精度。该软件将能够整合通过定向测序或其他方式生成的非鸟枪读取。它将增强环境样本的宏基因组组装。软件工程的改进将有助于算法的开发。为了使 Celera Assembler 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。