EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

被引：267

作者：

Miller, Christopher S. ^{[1
]}

Baker, Brett J. ^{[1
]}

Thomas, Brian C. ^{[1
]}

Singer, Steven W. ^{[2
,3
]}

Banfield, Jillian F. ^{[1
,4
]}

机构：

[1] Univ Calif Berkeley, Dept Earth & Planetary Sci, Berkeley, CA 94720 USA

[2] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Earth Sci, Berkeley, CA 94720 USA

[3] Joint BioEnergy Inst, Deconstruct Div, Emeryville, CA 94660 USA

[4] Univ Calif Berkeley, Dept Environm Sci Policy & Management, Berkeley, CA 94720 USA

来源：

GENOME BIOLOGY | 2011年 / 12卷 / 05期

关键词：

MAXIMUM-LIKELIHOOD; RARE BIOSPHERE; RNA GENES; DEEP-SEA; DIVERSITY; AMPLIFICATION; ALIGNMENT; GENOME; ULTRAFAST; WRINKLES;

D O I：

10.1186/gb-2011-12-5-r44

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Recovery of ribosomal small subunit genes by assembly of short read community DNA sequence data generally fails, making taxonomic characterization difficult. Here, we solve this problem with a novel iterative method, based on the expectation maximization algorithm, that reconstructs full-length small subunit gene sequences and provides estimates of relative taxon abundances. We apply the method to natural and simulated microbial communities, and correctly recover community structure from known and previously unreported rRNA gene sequences. An implementation of the method is freely available at https://github.com/csmiller/EMIRGE.

引用

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