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EMIRGE specifications


Unique identifier OMICS_12713
Alternative 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
Python, BioPython, Cython, pysam, scipy/numpy, usearch, samtools, bowtie
Maintained Yes




No version available



  • person_outline Christopher S Miller

Publications for Expectation-Maximization Iterative Reconstruction of Genes from the Environment

EMIRGE citations


Bioreactor microbial ecosystems with differentiated methanogenic phenol biodegradation and competitive metabolic pathways unraveled with genome resolved metagenomics

Biotechnol Biofuels
PMCID: 5946492
PMID: 29774049
DOI: 10.1186/s13068-018-1136-6

[…] Full-length or nearly-full-length 16S rRNA gene sequences were reconstructed from combined MP and AP metagenomes with EMIRGE [] by running the program against reference database SILVA SSU 119 [] clustered at 97% identity for 80 iterations. Reconstructed 16S rRNA gene sequences (> 1200 bp) post-chimera checking using […]


Hybridization capture reveals microbial diversity missed using current profiling methods

PMCID: 5870382
PMID: 29587880
DOI: 10.1186/s40168-018-0442-3

[…] ock community because of the bigger complexity of this soil sample.We then conducted operational taxonomic unit (OTU) reconstruction for the 16S rRNA genes from the three datasets using the dedicated EMIRGE software [] and classified them with the Silva [] database after chimera detection. At all taxonomic ranks, from domain to species, the community structures differed between the three methods ( […]


Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies

Sci Rep
PMCID: 5792648
PMID: 29386622
DOI: 10.1038/s41598-018-20414-0

[…]  = 1000 between 0 and 10000, selected K = 10000 between 10000 and 100000, selected K = 100,000 between 100,000 and 700,000).Assembly of shotgun reads assigned to the 16S rRNA gene was performed using EMIRGE. Sequences were clustered at 97% and 99% similarity using QIIME (1.9.0 + dfsg-0biolinux5) “pick_otus.py” software and taxonomy of the 16S rRNA sequences obtained were assigned using RDP classif […]


Metabolic capability and in situ activity of microorganisms in an oil reservoir

PMCID: 5756336
PMID: 29304850
DOI: 10.1186/s40168-017-0392-1

[…] .Ribosomal genes were identified using two complementary methods. In summary, (1) the dominant species (based on reconstructed near-full-length 16S rRNA gene) of each metagenome were identified using EMIRGE with default parameters [] and (2) rRNA_hmm [] was used to search assembled contigs containing 16S rRNA sequences. 16S rRNA sequences > 240 bp identified by EMIRGE and rRNA_hmm were combined fo […]


Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics

Proc Natl Acad Sci U S A
PMCID: 5776962
PMID: 29255014
DOI: 10.1073/pnas.1708779115
call_split See protocol

[…] assembled using paired-end Illumina HiSeq reads, and the assembly and prediction of ORFs were performed using the software tools MetaVelvet and Prokka (). 16S rRNA gene sequences were assembled using EMIRGE () and identified by BLASTn searching against the Silva SSU 128 database (). […]


Analysis of the cervical microbiome and potential biomarkers from postpartum HIV positive women displaying cervical intraepithelial lesions

Sci Rep
PMCID: 5727204
PMID: 29234019
DOI: 10.1038/s41598-017-17351-9
call_split See protocol

[…] arized at the species level. A rarefaction curve was constructed for each sample (Supplementary Figure ). The reconstruction of 16S consensus sequence was performed for a partial set of samples using EMIRGE, and taxa were assigned to consensus sequences using Blastn against the Greengenes Database. The resultant Blastn top hit (according to sorting criteria of the lowest e-value, highest bit-score […]


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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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