Development of Celera Whole Genome Shotgun Assembler

Celera 全基因组霰弹枪组装机的开发

• 批准号: 7068933
• 负责人: Granger Gideon Sutton
• 金额: $ 36.36万
• 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 2009-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7068933
• 关键词: computer assisted sequence analysis; computer program /software; computer system design /evaluation; genetic mapping; genome; information dissemination; molecular biology information system

DESCRIPTION (provided by applicant): The goal of this grant is to advance the genomic community's ability to accurately, easily and rapidly assemble genome sequences from shotgun sequencing data. Specifically, we plan to enhance and maintain a leading shotgun fragment assembly software program, the Celera Assembler. Shotgun DNA sequence data continues to be produced faster than it can accurately be assembled to determine genomic sequence. This problem will only be compounded as new sequencing machines, capable of producing large volumes of sequence data at low cost, come into active use. The sophistication of assembly software continues to be challenged to keep pace. The Celera Assembler was released into the public domain in 2004, and is managed as an open source project via the Sourceforge repository. The quality and accuracy of assembly software has a direct impact on the cost of genomic sequencing projects and genome closure, and the accuracy of the resulting genome sequence has a direct impact on all of the health related research that utilizes the sequence. We have assembled an exceptional team comprising a large portion of the original development team to improve and maintain the Celera Assembler, and support its user base. The principal investigator was the co-leader of the Celera Assembler development at Celera and the three co-investigators all made significant contributions to the algorithms and code base. This team has demonstrated that enhancements to the Celera Assembler could significantly improve the quality of genome assemblies (11, 41). This grant will allow us to make the Celera Assembler more user friendly, robust, capable of generating higher quality assemblies, and incorporating data from new types of sequencers. Towards this end, we will simplify and improve the algorithms and code, develop or incorporate analysis tools to assess the quality of assemblies, test the code on multiple computer platforms, debug the code on numerous organism assemblies, and develop a set of challenging benchmark assembly problems based on real data for use in rigorous regression testing to validate improved results using improved algorithms. All algorithmic improvements will be published in the scientific literature and documented in the code base. The entire code base and supporting analysis, benchmark and regression tools will be maintained as an open source project.

描述（由申请人提供）：这笔赠款的目的是提高基因组社区的能力，轻松，轻松，快速地从shot弹枪测序数据中组装基因组序列。具体而言，我们计划增强和维护领先的shot弹枪碎片组装软件程序Celera组装程序。 shot弹枪DNA序列数据的继续产生的速度比准确组装得出以确定基因组序列的速度更快。这个问题只会使其复合为新的测序机，能够以低成本生产大量序列数据，从而积极使用。汇编软件的复杂性继续受到挑战以保持步伐。 CELERA组装程序于2004年被释放到公共领域，并通过SourceForge存储库作为开源项目进行管理。组装软件的质量和准确性直接影响基因组测序项目和基因组封闭的成本，而所得基因组序列的准确性对利用该序列的所有健康相关研究都有直接影响。我们组建了一个杰出的团队，其中包括原始开发团队的大部分，以改善和维护Celera汇编程序，并支持其用户群。首席研究员是CELERA的CELERA汇编器开发的共同领导者，三个共同投资者都为算法和代码库做出了重要贡献。该团队已经证明，对Celera组装程序的增强功能可以显着提高基因组组件的质量（11，41）。该赠款将使我们能够使Celera组装程序更加用户友好，强大，能够生成更高质量的组件，并结合新类型的音序器的数据。为此，我们将简化和改进算法和代码，开发或合并分析工具来评估组件质量，在多个计算机平台上测试代码，对众多有机体组件进行调试代码，并基于一组具有挑战性的基准组装问题，基于一组真正的数据，以实现严格的回归测试，以验证改进的结果，以使用改进的量产生量化的杂志。所有算法的改进将在科学文献中发表，并记录在法规基础上。整个代码库以及支持分析，基准和回归工具将作为开源项目维护。