EMIRGE pipeline

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
Requirements Python, BioPython, Cython, pysam, scipy/numpy, usearch, samtools, bowtie
Maintained Yes



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  • person_outline Christopher S Miller <>

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

EMIRGE IN pipelines

PMCID: 5702734
PMID: 28800138
DOI: 10.1038/ismej.2017.128

[…] et al., 2011). relative abundances of operational taxonomic units (otus) detected in the 16s rrna amplicon libraries were highly correlated with 16s rrna gene abundances that were assembled using emirge (miller et al., 2011) from the metagenomes (data not shown)., protein extraction, digestion and mass spectrometry analysis followed previously reported protocols (bryson et al., 2016; […]

PMCID: 5041132
PMID: 27681823
DOI: 10.1038/srep34362

[…] 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: 4392516
PMID: 24468033
DOI: 10.1186/2049-2618-2-1

[…] of evolution with 100 bootstrap replicates., after sample preparation, 57 and 36 samples amplified successfully and were subsequently analyzed for infant 1 and infant 2, respectively (table 2). emirge generated approximately 12,000 full-length 16s rrna sequences and otus for each room-infant pair (clustered at the 97% nucleotide identity level). broadly speaking, species richness decreased […]

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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