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: 8103894
• 负责人: Jason Rafe Miller
• 金额: $ 59.12万
• 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 2013-09-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8103894
• 关键词: Address; Adoption; Algorithms; Biology; Characteristics; Chemistry; Chromosomes; Collection; Communities; Computer software; DNA; DNA Sequence; Data; Data Analyses; 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; Public Health; 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; cost effective; data modeling; forging; improved; interoperability; next generation; novel; open source; 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.

简介（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。所有的测序平台都依赖于复杂的装配软件来将一组reads转化为染色体长度序列。Celera Assembler是首屈一指的汇编器，10年来一直处于基因组学的前沿。它使桑格化学测序的真核生物基因组和宏基因组样品的开创性出版物成为可能。现在，Celera汇编器也支持454技术。Celera Assembler是最具侵略性的软件，可以从454个读取和配对数据集中构建和重复解析。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成为可能。该软件将在Sanger、454和混合数据集上显示出更好的性能和产量。该软件将获得在长读汇编过程中利用短读下一代数据的能力。它将获得纳入参考序列作为协助从头组装的能力。它的数据模型将被改进，以提高对真实数据的精度。该软件将能够整合由定向测序或其他方式产生的非霰弹枪读取。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、最终用户支持以及与数据源和分析工具集成的支持。

项目成果

Assembly algorithms for next-generation sequencing data.

• DOI: 10.1016/j.ygeno.2010.03.001
• 发表时间: 2010-06
• 期刊: GENOMICS
• 影响因子: 4.4
• 作者: Miller, Jason R.;Koren, Sergey;Sutton, Granger
• 通讯作者: Sutton, Granger

Aggressive assembly of pyrosequencing reads with mates.

• DOI: 10.1093/bioinformatics/btn548
• 发表时间: 2008-12-15
• 期刊: BIOINFORMATICS
• 影响因子: 5.8
• 作者: Miller, Jason R.;Delcher, Arthur L.;Koren, Sergey;Venter, Eli;Walenz, Brian P.;Brownley, Anushka;Johnson, Justin;Li, Kelvin;Mobarry, Clark;Sutton, Granger
• 通讯作者: Sutton, Granger

Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species.

两种高度多食性和入侵性 Helicoverpa 害虫物种进化和分化背后的基因组创新、转录可塑性和基因丢失

• DOI: 10.1186/s12915-017-0402-6
• 发表时间: 2017-07-31
• 期刊: BMC biology
• 影响因子: 5.4
• 作者: Pearce SL;Clarke DF;East PD;Elfekih S;Gordon KHJ;Jermiin LS;McGaughran A;Oakeshott JG;Papanicolaou A;Perera OP;Rane RV;Richards S;Tay WT;Walsh TK;Anderson A;Anderson CJ;Asgari S;Board PG;Bretschneider A;Campbell PM;Chertemps T;Christeller JT;Coppin CW;Downes SJ;Duan G;Farnsworth CA;Good RT;Han LB;Han YC;Hatje K;Horne I;Huang YP;Hughes DST;Jacquin-Joly E;James W;Jhangiani S;Kollmar M;Kuwar SS;Li S;Liu NY;Maibeche MT;Miller JR;Montagne N;Perry T;Qu J;Song SV;Sutton GG;Vogel H;Walenz BP;Xu W;Zhang HJ;Zou Z;Batterham P;Edwards OR;Feyereisen R;Gibbs RA;Heckel DG;McGrath A;Robin C;Scherer SE;Worley KC;Wu YD
• 通讯作者: Wu YD