Alignment Software for Second-Generation Sequencing

描述（由申请人提供）：最新一代的DNA测序技术已经刺激了使用测序来回答生物学和医学中的基本问题的巨大增长。全基因组测序被用于研究癌症，研究人类基因组中常见的致病变异，并更好地了解人类多样性。通过称为RNA-seq的协议对信使RNA进行测序，导致了许多项目的爆炸，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序列与参考基因组进行比对，并帮助解释结果。我们的团队已经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比对程序; TopHat，一个跨内含子比对剪接转录本（mRNA）的比对程序;和Cufflinks，一个从TopHat产生的比对中组装完整转录本（包括可变剪接变体）的程序。我们的工具旨在处理非常大的下一代序列数据集，将以前工具需要多个CPU天的比对时间减少到几分钟。它们也有相对适中的内存需求，允许它们在台式计算机上运行。由于这些和其他原因，这些程序已经成为许多研究小组的首选工具;仅Bowtie程序就已经吸引了非常庞大的用户群，自2008年首次发布以来，下载量超过20，000次。在这项提案中，我们要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，并增加旨在改善比对和协助研究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.