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: 10303035
• 负责人: Mihai Pop
• 金额: $ 70.3万
• 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 2023-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10303035
• 关键词: Address; Algorithmic Software; Algorithms; Biological; Chromosomes; Collection; Communities; Complement; Complex Mixtures; DNA Modification Process; Data; Devices; Disease; Effectiveness; Elements; Emerging Technologies; Future; Genes; Genome; Genomic Segment; Genomics; Graph; Health; Hi-C; High-Throughput Nucleotide Sequencing; Human; Individual; Label; Laboratories; Lead; Light; Link; Manuals; Measures; Metagenomics; Methods; Microbe; Molecular Conformation; Operon; Organism; Pattern; Play; Regulatory Element; Research; Role; Sampling; Software Tools; Source; Speed; Structure; Taxonomy; Technology; Time; Validation; Variant; Visual; base; computerized tools; contig; deep sequencing; experience; improved; metagenome; microbial community; microbial genome; nanopore; novel strategies; programs; rRNA Genes; reconstruction; reference genome; scale up; success; targeted sequencing; tool; user friendly software; whole genome

Abstract Through this proposal, we will develop new computational tools for reconstructing nearly- complete microbial genomes from complex mixtures, as well as their strain structure. We will build upon our initial successes in developing metagenomic assembly algorithms capable of characterizing strain variants (7, 8), as well as upon our experience in using co-abundance across samples to link/bin together genes originating from the same organism (9). In addition, we will develop algorithms able to use information generated by emerging technologies, such as chromosome conformation information generated by Hi-C (10-12), or information about DNA modifications as generated by new nanopore sequencing devices(13, 14).

摘要 通过这项提案，我们将开发新的计算工具来重建近- 从复杂的混合物中提取完整的微生物基因组，以及它们的菌株结构。我们 将建立在我们最初成功开发宏基因组组装算法的基础上， 表征菌株变体（7，8），以及基于我们在使用跨 将来自同一生物体的基因连接/结合在一起的样本（9）。此外，我们将 开发能够使用新兴技术产生的信息的算法，例如 由Hi-C（10-12）产生的染色体构象信息，或关于DNA的信息 通过新的纳米孔测序装置产生的修饰（13，14）。