Development of a Rapid Processing Pipeline and Graph-based Visualization for the Analysis of Next Generation Sequencing Data

在过去十年左右的时间里，从新的实验室分析平台产生的生物数据呈爆炸式增长。这些数据日益复杂和大规模。特别是DNA测序在过去的十年里给生物医学和生物科学带来了革命性的变化。最近新的DNA测序平台的出现意味着，与几年前相比，可以产生更多数量级的数据。这些进展进一步改变了我们对基础、应用和临床研究的科学方法的思考方式。例如，对许多相关生物的整个基因组进行排序的能力使大规模的比较和进化研究得以进行，这些研究直到最近还是不可想象的。通过用于基因表达分析的RNA测序，测序也可以用来确定哪些基因在任何给定的状态或时间都是活跃的。在分析基因表达研究中，RNA测序可以在不事先知道的情况下识别和量化稀有基因，并可以提供有关已识别基因中序列变异的信息。当与“下拉”技术相结合时，这些方法还可以回答有关基因调控的重要问题，如转录因子或microRNA靶标结合。然而，技术上的这些进步带来了重大的分析挑战，特别是在目前正在产生的数据的绝对规模方面。例如，一台Illumina Solexa GA-2机器的单次运行就产生了大约100 GB的序列数据。对这些数据的分析有许多方法，但这些方法通常很慢，而且计算非常密集，需要大内存计算机或高性能计算集群才能有效地分析这些数据。如何最好地分析这些信息是一个正在进行的积极讨论。解决其中一些问题的一种方法是开发用于数据分析的快速优化算法，并以网络图的形式可视化和分析数据。这项建议是为了开发一个优化的系统来分析这些数据。它将涉及到开发极快和优化的算法来处理我们已经为其创建原型的数据。我们将利用相对较新的GPU硬件加速领域，使这些算法在使用消费类3D显卡上的专用硬件时运行得更快。通过该系统处理的数据将使用围绕现有BioLayout Express3D系统设计的定制3D可视化环境进行可视化。这些序列图已经证明它们自己有助于识别新的序列元件并帮助组装它们的共同序列，在许多情况下有助于识别问题所在。此外，我们打算利用相关分析的力量来处理RNA-SEQ数据，为从初级序列数据到每个基因摘要标签的共同表达分析提供一个集成的解决方案。然而，在这样做的同时，我们还将提供主要数据的基于网络和比对的视图，这些视图是摘要分析的基础。这将为用户提供新的方式来查看他们的数据，以及读取如何相互作用和基因组本身。整个系统将是模块化的，每个模块将从用Java编写的图形用户界面访问，这使用户能够控制分析模块，并允许快速分析从原始数据到基因组/基因水平的大规模数据集。

Over the last decade or so there has been an explosion of biological data emanating from new laboratory analysis platforms. These data are increasingly complex and large-scale. DNA sequencing in particular has revolutionized the biomedical and biological sciences over the last decade. The recent availability of new DNA sequencing platforms mean that orders of magnitude more data can be produced relative to what was possible just a few years ago. These advances have further changed the way we think about scientific approaches to basic, applied and clinical research. For example, the ability to sequence the whole genome of many related organisms has allowed large-scale comparative and evolutionary studies to be performed that were until recently unimaginable. Sequencing can also be used to determine which genes are currently active at any given state or time by RNA sequencing for gene-expression analyses. In analysing gene-expression studies, RNA-sequencing can identify and quantify rare genes without prior knowledge and can provide information regarding sequence variation in the identified genes. When combined with 'pull-down' technologies, these approaches can also answer important questions regarding gene regulation such as transcription factor or microRNA target binding. These advances in technology however come with significant analytical challenges, in particular with respect to the sheer scale of data now being produced. For example a single run of an Illumina Solexa GA-2 machine produces approximately 100Gb of sequence data alone. A number of approaches exist for the analysis of these data, however they are usually slow and extremely computationally intensive, requiring large-memory computers or high-performance computing clusters in order to effectively analyse these data. How best to analyse this information is an ongoing and active discussion. One approach to resolving some of these issues is to both develop fast optimal algorithms for data analysis and to visualise and analyse data as network graphs. This proposal is to develop an optimised system for the analysis of such data. It will involve the development of extremely fast and optimised algorithms for processing the data for which we have already created prototypes. We will utilise the relatively new field of GPU hardware acceleration to allow these algorithms to run significantly faster when utilising specialised hardware on a consumer 3D graphics card. Data processed through the system will be visualised using a customised 3D visualisation environment designed around the existing BioLayout Express3D system. These sequence graphs have already proved themselves useful identifying novel sequence elements and aiding the assembly of their consensus sequences, in many cases helping to identify where issues lie. Furthermore, we intend to harness the power of correlation analysis for working with RNA-seq data, providing an integrated solution for moving from primary sequence data through to co-expression analysis of tags per gene summaries. In doing however we will also provide network and alignment based views of the primary data that underpin the summary analyses. This will provide novel ways for users to see their data and how reads interact with each other and the genome itself. The entire system will be modular and each module will be accessed from a graphical user interface written in Java, that gives the user control over analysis modules and allows rapid analysis of large-scale datasets from the primary data to genome/gene level analyses.