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DOI | 10.1038/s41467-017-02515-y |
Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps | |
Dilthey, Alexander T.1,2; Jain, Chirag2,3; Koren, Sergey2; Phillippy, Adam M.2 | |
2019-07-11 | |
发表期刊 | NATURE COMMUNICATIONS
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ISSN | 2041-1723 |
出版年 | 2019 |
卷号 | 10 |
文章类型 | Article |
语种 | 英语 |
国家 | Germany; USA |
英文摘要 | Metagenomic sequence classification should be fast, accurate and information-rich. Emerging long-read sequencing technologies promise to improve the balance between these factors but most existing methods were designed for short reads. MetaMaps is a new method, specifically developed for long reads, capable of mapping a long-read metagenome to a comprehensive RefSeq database with > 12,000 genomes in < 16 GB or RAM on a laptop computer. Integrating approximate mapping with probabilistic scoring and EM-based estimation of sample composition, MetaMaps achieves > 94% accuracy for species-level read assignment and r(2) > 0.97 for the estimation of sample composition on both simulated and real data when the sample genomes or close relatives are present in the classification database. To address novel species and genera, which are comparatively harder to predict, MetaMaps outputs mapping locations and qualities for all classified reads, enabling functional studies (e.g. gene presence/absence) and detection of incongruities between sample and reference genomes. |
领域 | 资源环境 |
收录类别 | SCI-E |
WOS记录号 | WOS:000474824900006 |
WOS关键词 | PHYLOGENETIC CLASSIFICATION ; FAST GENOME ; SEQUENCES ; GENE ; TIME ; TOOL |
WOS类目 | Multidisciplinary Sciences |
WOS研究方向 | Science & Technology - Other Topics |
URL | 查看原文 |
引用统计 | |
文献类型 | 期刊论文 |
条目标识符 | http://119.78.100.173/C666/handle/2XK7JSWQ/203624 |
专题 | 资源环境科学 |
作者单位 | 1.Heinrich Heine Univ Dusseldorf, Inst Med Microbiol & Hosp Hyg, Dusseldorf, North Rhine Wes, Germany; 2.NHGRI, Genome Informat Sect, Computat & Stat Genom Branch, Bethesda, MD 20892 USA; 3.Georgia Inst Technol, Atlanta, GA 30332 USA |
推荐引用方式 GB/T 7714 | Dilthey, Alexander T.,Jain, Chirag,Koren, Sergey,et al. Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps[J]. NATURE COMMUNICATIONS,2019,10. |
APA | Dilthey, Alexander T.,Jain, Chirag,Koren, Sergey,&Phillippy, Adam M..(2019).Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps.NATURE COMMUNICATIONS,10. |
MLA | Dilthey, Alexander T.,et al."Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps".NATURE COMMUNICATIONS 10(2019). |
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