Journal
GENOME BIOLOGY
Volume 12, Issue 5, Pages -Publisher
BMC
DOI: 10.1186/gb-2011-12-5-r44
Keywords
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Funding
- Genome Sciences Program in Carbon Cycling [DE-SC0004665]
- Systems Biology Knowledgebase [DE-SC0004918]
- US Department of Energy, Office of Science, Office of Biological and Environmental Research
- US Department of Energy, Office of Science, Office of Biological and Environmental Research, through Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]
- US Department of Energy, Office of Science, Office of Biological and Environmental Research, through US Department of Energy [DE-AC02-05CH11231]
- Office of Science of the US Department of Energy [DE-AC02-05CH11231]
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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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