Computational Methods for Microbial and Microbiome Sequence Analysis

项目摘要 该项目将支持我们在微生物序列分析的计算方法方面的工作，包括基因 发现、全基因组比对、基因组组装和元基因组序列分析。多年来，我们 开发了多种系统来解决这些领域的问题，其中一些系统得到了非常广泛的应用。这些 工具需要不断更新和改进，以跟上测序技术的变化、变化 在实验设计方面，以及不断增长的测序基因组数量。其中一个系统是微光系统， 在细菌、病毒、古菌和简单的真核生物中寻找基因的一种计算方法。微光是 非常准确，在大多数原核生物基因组中找到了99%以上的基因。它已经被数以千计的 世界各地的科学家和在过去发表的大多数细菌基因组测序项目 十年。描述Gimmer的三篇主要出版物总共被引用了4700多次， 仅在2016-17年度，就包括了700次引文。近年来，微光的使用有所增加，原因是 下一代测序项目的爆炸性增长，这对细菌基因组来说特别具有成本效益。一个 第二个系统，木乃伊，是一种高效的全基因组比对系统，用于比较基因组之间的关系。 并比较基因组组合以检测变化，无论是大的还是小的。木乃伊及其成分， 尤其是Nucmer，已经被广泛应用于其他系统，包括多基因组比对系统 和几个基因组组装包。描述木乃伊的三种主要出版物被引用 超过3600次，其中包括2016-17年度的750次引用。近年来，我们将努力集中在 开发元基因组数据的分析方法，生产几种较新的工具，包括Kraken 还有离心机。这两个系统都试图为元基因组学中的每个读数分配一个物种标识符 数据集。因为Kraken算法不仅准确，而且比以前的方法快得多，所以它很快 在它发布后不久就被许多实验室采用，并且它的使用持续增长。更新更大的空间- 高效的离心机系统也非常成功，最近被纳入分析 其中一家新的第三代测序公司的包装。我们将继续致力于改善 这两种算法的性能，这个项目将允许我们扩展它们来处理最新的长读 越来越多的数据被用于元基因组学实验。最后，实验室的一个新方向是使用 用于诊断感染的超基因组鸟枪测序，我们不仅修改了我们的 算法，而且还建立定制的基因组数据库，在其中我们严格筛选基因组以识别 并去除产生假阳性的污染物和低复杂性序列。就像我们为许多人所做的那样 几年后，我们将在开放源码下免费发布这个项目产生的所有软件和数据 许可，允许其他科学家不受任何限制地使用、修改和重新分发它们。

Project Summary This project will support our work on computational methods for microbial sequence analysis, including gene finding, whole-genome alignment, genome assembly, and metagenomic sequence analysis. Over the years we have developed multiple systems to solve problems in these areas, some of which are very widely used. These tools need continued updates and improvements to keep pace with changes in sequencing technology, changes in experimental design, and the ever-growing number of sequenced genomes. One of these systems is Glimmer, a computational method for finding genes in bacteria, viruses, archaea, and simple eukaryotes. Glimmer is highly accurate, finding over 99% of the genes in most prokaryotic genomes. It has been used by thousands of scientists around the world and in the majority of published bacterial genome sequencing projects over the past decade. Collectively the three main publications describing Glimmer have been cited over 4,700 times, including >700 citations in 2016-17 alone. Usage of Glimmer has been increased in recent years due to the explosion in next-generation sequencing projects, which are particularly cost-effective for bacterial genomes. A second system, MUMmer, is an efficient whole-genome aligner that is used to compare genomes to one another and to compare genome assemblies to detect changes, both large and small. MUMmer and its components, especially Nucmer, have been widely used and incorporated in other systems, including multi-genome aligners and several genome assembly packages. The three main publications describing MUMmer have been cited over 3,600 times including >750 citations in 2016-17. In recent years we have focused our efforts on developing methods for the analysis of metagenomics data, producing several newer tools, including Kraken and Centrifuge. Both of these systems attempt to assign a species identifier to every read in a metagenomics data set. Because the Kraken algorithm is not only accurate but far faster than earlier methods, it was rapidly adopted by many labs soon after its release, and its usage continues to grow. The even newer and more space- efficient Centrifuge system has also been highly successful and was recently incorporated into the analysis package of one of the new third-generation sequencing companies. We continue to work on improving the performance of both algorithms, and this project will allow us to extend them to handle the newest long-read data that is increasingly being used for metagenomics experiments. Finally, a new direction of the lab is the use of metagenomic shotgun sequencing to diagnose infections, for which we are not only modifying our algorithms, but also building customized genome databases where we rigorously screen the genomes to identify and remove contaminants and low-complexity sequences that create false positives. As we have done for many years, we will release all of the software and data generated by this project for free under an open source license, allowing other scientists to use, modify, and redistribute them without restrictions of any kind.