Continued Improvements of Whole Genome Shotgun Assembly

描述（由申请人提供）：我们的目标是开发一套独立于所使用的装配软件的预处理和后处理工具，因此可以立即在所有主要的测序/装配中心实施。我们将使我们的软件和方法免费提供，开源。预处理：具体目标1。通过更好地利用读取数据来改善基因组组装草图。(a)载体修剪：不正确修剪的载体序列经常导致基因组组装不必要地断裂。我们提出了一种改进的矢量修剪方法，可以自动确定矢量序列。(b)我们建议对读取数据进行预处理，以增加读取数据3'端可用序列的数量，使用基于重叠的误差校正，然后使用基于重叠的修剪。我们建议在reads的3'端使用低质量碱基来帮助识别重复区域。此程序将用于进一步改善UMD重叠。(c)我们建议使用我们的读取扩展和错误纠正程序来创建更好的低测序基因组组装。后处理：我们建议开发一套与装配器无关的技术，可以在任何测序/装配中心或任何测序联盟的框架中使用。具体目标2。装配评估软件。我们已经开发了压缩/膨胀（CE）统计，使我们能够检测草稿组件中的错误组装区域。我们还开发了一种软件，使用射击方法来确定哪些插入物位于易于组装的（不一定是唯一的）基因组区域，并精确测量它们的大小。我们建议开发集成装配评估/错误装配检测软件，该软件使用基于读取和配对位置的统计数据以及从射击方法中获得的数据来检测草稿装配中的问题。具体目标3。组装和解。我们建议创建一个软件，通过使用不同的汇编程序或使用不同参数的相同汇编程序从相同的读取数据创建的相同基因组的替代草稿汇编来增强给定的草稿汇编。美国政府在全基因组鸟枪测序上花费了数亿美元。我们相信，如果这个项目的目标得以实现，将会产生更好、更便宜的基因组。与生成读取的成本相比，使用我们的技术的成本可以忽略不计。我们的方法可能会发现更多的基因和调控区域，从而更好地了解各种基因组的遗传结构。该项目的最终目标是通过更好地了解人类基因组和其他物种的基因组来改善公众健康。

DESCRIPTION (provided by applicant): Our goal is to develop a set of pre- and post-processing tools that are independent of the assembly software used and thus could be immediately implemented at all major sequencing/assembly centers. We will make our software and methods freely available, open source. Pre-processing: Specific Aim 1. Improving draft genome assemblies through better use of read data, (a) Vector Trimming: Improperly trimmed vector sequences often cause genome assemblies to break unnecessarily. We propose an improved vector trimming method that determines vector sequence automatically, (b) We propose to preprocess the read data to increase the amount of useable sequence on the 3' ends of the reads using overlap-based error correction followed by overlap-based trimming. We propose to use low quality bases on the 3' ends of the reads to help resolve repetitive regions. This procedure would be used to further improve UMD Overlapper. (c) We propose to use our read extension and error correction routines to create better assemblies of genomes sequenced at low. Post-processing:We propose to develop a set of assembler-independent techniques that can be used at any sequencing/assembly center or in the framework of any sequencing consortium. Specific Aim 2. Assembly evaluation software. We have developed a Compression/Expansion (CE) statistic that allows us to detect misassembled regions in the draft assemblies. We also developed software that uses shooting method to determine which inserts lie in easy to assemble (not necessarily unique) regions of the genome and exactly measure their size. We propose to develop integrated assembly evaluation/misassembly detection software that uses statistics based on read and mate pair placements and data obtained from the shooting methods to detect problems in draft assemblies. Specific Aim 3. Assembly reconciliation. We propose to create software that enhances a given draft assembly using alternate draft assemblies of the same genome created from the same read data with different assembly programs, or with the same assembly program using different parameters. The U.S. government spends hundreds of millions of dollars on whole genome shotgun sequencing. We believe that if the goals of this project are achieved, significantly better and cheaper genomes will be produced. The cost of using our techniques will be negligible compared to the cost of generating reads. Our approach may find more genes and regulatory regions and lead to a better understanding of the genetic structure of the various genomes. The ultimate goal of this project is to improve public health by better understanding the human genome and the genomes of other species.