EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing...
EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
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Publisher
England: BioMed Central Ltd
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Language
English
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Publisher
England: BioMed Central Ltd
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Contents
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....
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Full title
EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
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Record Identifier
TN_cdi_proquest_miscellaneous_900629703
Permalink
https://devfeature-collection.sl.nsw.gov.au/record/TN_cdi_proquest_miscellaneous_900629703
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ISSN
1474-760X
E-ISSN
1474-760X
DOI
10.1186/gb-2011-12-5-r44
