EMIRGE specifications


Unique identifier OMICS_12713
Name Expectation-Maximization Iterative Reconstruction of Genes from the Environment
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data EMIRGE takes as inputs the raw reads and quality values from a short-read DNA sequencing project and an initial large database of curated small subunit sequences.
Input format FASTQ
Biological technology Illumina
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Requirements Python, BioPython, Cython, pysam, scipy/numpy, usearch, samtools, bowtie
Maintained Yes



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  • person_outline Christopher S Miller <>

EMIRGE articles

EMIRGE citations

PMCID: 5041132

[…] and many short contigs (n50 2.6 and 1.6 kbp for ab1_ovicells and mhd_larvae, respectively, supplementary table s1). reconstruction of 16s rrna gene sequences from ab1_ovicells sequence reads using emirge3132, however, revealed evidence of multiple bacteria in addition to ca. e. sertula (supplementary table s2). these additional genomes were found in ab1_ovicells, but not mhd_larvae, meaning […]

PMCID: 4784552

[…] showed higher proportional abundance of rare taxa, probably as the result of variation in genome sizes across all taxa. reconstruction of 16s rrna gene sequences from the metagenomic dataset with emirge (miller et al., 2011) provided full-length, or nearly full-length, genes for all the major phyla observed in the 16s rrna gene dataset (supplementary figure s3) that also indicated […]

EMIRGE institution(s)
Department of Earth and Planetary Science, University of California, Berkeley, CA, USA; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA; Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, USA

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