Algorithms and Software for the Assembly of Metagenomic Data

用于宏基因组数据组装的算法和软件

• 批准号: 8640071
• 负责人: Mihai Pop
• 金额: $ 43.5万
• 依托单位: UNIV OF MARYLAND, COLLEGE PARK
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-03-21 至 2017-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8640071
• 关键词: Algorithmic Software; Algorithms; Area; Bacteria; Clinical; Code; Communities; Complex; Computer software; DNA Sequence; Data; Data Analyses; Data Set; Detection; Development; Disease; Ensure; Future; Genes; Genetic Materials; Genome; Genomic Segment; Genomics; Goals; Health; High-Throughput Nucleotide Sequencing; Human; Human body; Individual; Link; Maps; Metagenomics; Microbe; Modeling; Molecular; Organism; Play; Procedures; Recombinant DNA; Research Infrastructure; Research Personnel; Ribosomal RNA; Role; Running; Sampling; Structure; Surveys; Technology; Testing; Time; Validation; Variant; Viral; base; comparative; flexibility; interest; metagenome; microbial community; microbial disease; microbiome; novel; novel strategies; open source; programs; public health relevance; rRNA Genes; reconstruction; software development; tool

DESCRIPTION (provided by applicant): The goal of the current proposal is to develop a new flexible framework for metagenomic assembly. This framework will provide novel algorithms for de novo and comparative assembly of metagenomic data, as well as tools for extracting and analyzing genomic variation. In addition, a novel approach will be developed for reconstructing segments of a genome containing a specific 16S rRNA sequence. At the core of this framework are two packages developed in the PIs lab: the open source package AMOS - a flexible and modular assembly package, and Bambus 2 - a genomic scaffolder specifically targeted at metagenomic data. A novel model-based testing framework will be closely integrated with the developments proposed here in order to ensure the correctness of the software being developed. Several levels of test procedures will be run every time the code is changed, on a nightly basis, as well as at regular intervals, allowing errors to be promptly discovered and corrected.

描述（由申请人提供）：当前提案的目标是开发用于宏基因组组装的新的灵活框架。该框架将为宏基因组数据的从头和比较组装提供新的算法，以及提取和分析基因组变异的工具。此外，将开发一种新的方法来重建含有特定16 S rRNA序列的基因组片段。这个框架的核心是PI实验室开发的两个软件包：开源软件包AMOS -一个灵活的模块化组装软件包，以及Bambus 2 -一个专门针对宏基因组数据的基因组支架。一个新的基于模型的测试框架将紧密结合在一起，以确保正在开发的软件的正确性，在这里提出的发展。每次代码更改时，将运行几个级别的测试程序，每晚以及定期运行，以便及时发现和纠正错误。