AF: Medium: Parallel Algorithms and Software for High-Throughput Sequence Assembly

高通量下一代 DNA 测序技术 (NGS) 允许快速且经济高效地对基因组和转录组（表达的基因组序列）进行采样，正在引发生命科学研究的重大革命。从数十亿个这样的随机采样序列中组装基因组和转录组是计算生物学中的一个重要问题。尽管已经取得了重大进展，但在解决多样化和快速新兴的平台、提高组装质量以及扩展到大规模数据大小和大型基因组方面仍有大量工作要做。该项目将利用高性能计算的力量来开发有效的序列组装解决方案。它将导致可扩展、高效的并行算法以及用于基因组和转录组组装的并行集成软件框架的开发。该项目旨在通过解决重要的未解决问题（例如来自多个 NGS 平台的序列的混合组装）、取得基本算法进步以提高组装质量以及针对与组装相关的所有问题进行并行算法开发来深入努力，从而推动最先进的技术发展。该项目将由跨学科研究团队与领先的 NGS 制造商和参与大型植物基因组测序项目的院士合作进行。该项目将导致发布用于序列组装的可扩展并行软件包，该软件包将提供给科学界。博士后和研究生将接受计算机科学驱动的跨学科研究和编写高效高性能计算软件的培训。该项目将影响课程开发，并将产生用于下一代测序的生物信息学教育材料。

High-throughput next-generation DNA sequencing technologies (NGS) are causing a major revolution in life sciences research by allowing rapid and cost-effective sampling of genomes and transcriptomes (expressed genomic sequences). Assembly of genomes and transcriptomes from billions of such randomly sampled sequences is an important problem in computational biology. While significant strides have been made, much work remains in addressing the diverse and rapidly emerging platforms, improving assembly quality, and scaling to both large-scale data sizes and large genomes. This project will harness the power of high performance computing to develop effective solutions for sequence assembly. It will lead to the development of scalable, efficient parallel algorithms and a parallel integrated software framework for genome and transcriptome assembly. The project seeks to advance the state of the art by targeting important unsolved problems such as hybrid assembly of sequences from multiple NGS platforms, making fundamental algorithmic advances to improve assembly quality, and conducting an in-depth effort at parallel algorithms development for the entire gamut of problems that arise in connection with assembly. It will be carried out by an interdisciplinary team of investigators, in partnership with leading NGS manufacturers and academicians involved in large plant genome sequencing projects. The project will lead to the release of a scalable parallel software package for sequence assembly that will be made available to the scientific community. Postdoctoral and graduate students will be trained in computer science driven interdisciplinary research and in writing efficient high performance computing software. The project will influence curriculum development and will lead to educational materials in bioinformatics for next-generation sequencing.