Work

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

Year: 2011

Type: article

Abstract: 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.

Source: Genome biology

DOI: 10.1186/gb-2011-12-5-r44

Authors: Christopher S Miller, Brett J Baker, Brian C Thomas, Steven W Singer, Jillian F Banfield

Institutions: University of California, Berkeley, Lawrence Berkeley National Laboratory, Joint BioEnergy Institute

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $5,490