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

高通量下一代DNA测序技术(NGS)通过快速和经济有效地对基因组和转录体(表达的基因组序列)进行采样，正在引发生命科学研究的一场重大革命。从数十亿个这样的随机抽样序列中组装基因组和转录本是计算生物学中的一个重要问题。虽然已经取得了重大进展，但在解决多样化和快速崛起的平台、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许多工作要做。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。它将导致可扩展的、高效的并行算法的开发，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。该项目旨在通过瞄准重要的未解决问题，如来自多个NGS平台的序列的混合组装，进行基本的算法进步以提高组装质量，并对与组装相关的所有问题进行深入的并行算法开发，从而推动最新技术的发展。它将由一个跨学科的研究小组进行，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。该项目将导致一个可扩展的用于序列组装的并行软件包的发布，并将向科学界提供。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，并将为下一代测序提供生物信息学教材。

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.