Development of Celera Whole Genome Shotgun Assembler

Celera 全基因组霰弹枪组装机的开发

• 批准号: 7232125
• 负责人: Granger Gideon Sutton
• 金额: $ 36.38万
• 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/7232125
• 关键词: Algorithms; Benchmarking; Closure; Code; Communities; Computer software; Computers; Consult; DNA Sequence; Data; Development; Disease regression; Engineering; Ensure; Environment; Future; Genome; Genomics; Goals; Grant; Health; Literature; Maintenance; Monitor; Numbers; Organism; Output; Principal Investigator; Process; Public Domains; Publishing; Reporting; Research; Research Personnel; Resources; Role; Shotgun Sequencing; Shotguns; Source; Techniques; Testing; Thinking; Validation; Work; base; cost; genome sequencing; improved; insight; microbial genome; open source; programs; repository; theories; tool; user-friendly

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(由申请者提供)：这项资助的目标是提高基因组社区从鸟枪式测序数据中准确、容易和快速地组装基因组序列的能力。具体地说，我们计划增强和维护领先的猎枪碎片组装软件程序--Celera汇编程序。猎枪DNA序列数据的产生速度继续快于准确组装以确定基因组序列的速度。随着能够以低成本产生大量序列数据的新型测序机投入使用，这个问题只会变得更加复杂。组装软件的复杂程度继续受到挑战，以跟上步伐。Celera汇编器于2004年发布到公共领域，并通过Sourceforge存储库作为开放源码项目进行管理。组装软件的质量和准确性直接影响到基因组测序项目和基因组关闭的成本，而得到的基因组序列的准确性直接影响到利用该序列进行的所有与健康相关的研究。我们组建了一个由大部分原始开发团队组成的特殊团队，以改进和维护Celera汇编器，并支持其用户基础。首席调查员是Celera汇编器开发的联合负责人，三名联合调查员都对算法和代码库做出了重大贡献。该团队已经证明，对Celera组装器的增强可以显著提高基因组组装器的质量(11，41)。这笔赠款将允许我们使Celera汇编程序更加用户友好、更强大，能够生成更高质量的汇编程序，并纳入来自新型测序仪的数据。为此，我们将简化和改进算法和代码，开发或整合分析工具来评估汇编的质量，在多个计算机平台上测试代码，在众多生物体汇编上调试代码，并根据实际数据开发一系列具有挑战性的基准汇编问题，用于严格的回归测试，以验证使用改进算法的改进结果。所有的算法改进都将发表在科学文献中，并记录在代码库中。整个代码库和辅助分析、基准和回归工具将作为开放源码项目进行维护。