Alignment Software for Second-Generation Sequencing

描述（由申请人提供）：最新一代的DNA测序技术刺激了测序在回答生物学和医学基本问题方面的巨大增长。全基因组测序正被用于研究癌症，研究人类基因组中常见的致病变异，并更好地描绘人类多样性。通过被称为RNA-seq的协议对信使RNA进行测序，导致了许多项目的爆发，以表征许多物种中许多细胞类型的转录组。这些基于测序的研究产生了大量的数据，这反过来又需要复杂、高效的计算工具来将DNA序列与参考基因组对齐，并帮助解释结果。我们的团队开发了一套软件工具，用于将DNA和RNA与参考基因组进行比对。其中包括Bowtie，一个非常快速的短读对齐程序；TopHat是一种比对程序，用于比对内含子间的剪接转录物（mRNA）；以及Cufflinks，这是一个从TopHat产生的比对中组装完整转录本的程序，包括可选择的剪接变体。我们的工具设计用于处理非常大的下一代序列数据集，将以前的工具需要多个cpu天的校准时间缩短到几分钟。它们对内存的要求也相对较低，因此可以在台式电脑上运行。由于这些和其他原因，这些程序已成为许多研究小组的首选工具；Bowtie程序本身就已经吸引了庞大的用户群，自2008年首次发布以来，下载量已超过2万次。在本提案中，我们请求支持维护这些开源软件程序，使其适应不断变化的DNA测序技术，并添加旨在改进比对并协助调查人员进行分析的新功能。

DESCRIPTION (provided by applicant): The latest generation of DNA sequencing technology has spurred a tremendous increase in the use of sequencing to answer fundamental questions in biology and medicine. Whole-genome sequencing is being used to study cancer, to study common disease-causing variants in the human genome, and to create a better picture of human diversity. Sequencing of messenger RNA through the protocol known as RNA-seq has led to an explosion of projects to characterize the transcriptome of many cell types in many species. These sequencing-based studies generate enormous amounts of data, which in turn require sophisticated, efficient computational tools to align the DNA sequence back to a reference genome and to help interpret the results. Our group has developed a suite of software tools for alignment of DNA and RNA to a reference genome. These include Bowtie, a very fast short-read alignment program; TopHat, an alignment program that aligns spliced transcripts (mRNA) across introns; and Cufflinks, a program that assembles complete transcripts, including alternative splice variants, from the alignments that TopHat produces. Our tools have been designed to handle very large next-generation sequence data sets, reducing alignment times that took multiple CPU-days with previous tools to just minutes. They also have relatively modest memory requirements, allowing them to be run on a desktop computer. For these and other reasons, these programs have become the preferred tools for numerous research groups; the Bowtie program alone has already attracted a very large user base, with over 20,000 downloads since its initial release in 2008. In this proposal, we ask for support to maintain these open-source software programs, adapt them to continuously changing DNA sequencing technology, and add new features designed to improve the alignments and to assist investigators with their analyses.