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MIRA specifications


Unique identifier OMICS_00023
Alternative names Mimicking Intelligent Read Assembly, MIRA assembler
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Life Technologies, Pacific Biosciences, Roche
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes




No version available



  • person_outline Bastien Chevreux <>

Publication for Mimicking Intelligent Read Assembly

MIRA citations


Transcript expression plasticity as a response to alternative larval host plants in the speciation process of corn and rice strains of Spodoptera frugiperda

PMCID: 5644112
PMID: 29037161
DOI: 10.1186/s12864-017-4170-z

[…] assembler suite []. a de novo hybrid assembly using ests data from the spodobase project (http://bioweb.ensam.inra.fr/spodobase/) and in-house illumina sequencing reads was performed with the mira assembler v. 4.9.3 [] with two passes and the following settings: i) spoiler detection on (−as:sd = yes), ii) 70% relative percentage of exact word matches (−sk:pr = 70), iii) maximum megahub […]


Identification and Characterization of Odorant Binding Proteins in the Forelegs of Adelphocoris lineolatus (Goeze)

PMCID: 5623005
PMID: 29018358
DOI: 10.3389/fphys.2017.00735

[…] using the mira3.0 (chevreux et al., ) and cap3 software programs (huang and madan, ) with default parameters. two steps were performed to assemble the clean reads. first, the sequence assembler mimicking intelligent read assembly mira3 was used with the assembly settings of a minimum sequence overlap of 30 bp and a minimum percentage overlap identity of 80%. then, contig assembly program […]


Re Assembly and Analysis of an Ancient Variola Virus Genome

PMCID: 5618019
PMID: 28885569
DOI: 10.3390/v9090253

[…] sequence by using alternative assembly strategies. our first attempts at assembling the data provided by the sequence read archive (srp091673), using cutadapt [] to trim illumina adapters and mira (mimicking intelligent read assembly) [] and spades (st. petersburg genome assembler) [] for assembly, created 56 contigs that could not be resolved by modifying the assembly parameters. however, […]


Draft whole genome sequence of groundnut stem rot fungus Athelia rolfsii revealing genetic architect of its pathogenicity and virulence

PMCID: 5509663
PMID: 28706242
DOI: 10.1038/s41598-017-05478-8

[…] v4.0.2 followed by cap3 (table ). the estimated genome size of ~63.64 mb was obtained by k-mergenie software with optimal k-mer size of 57 (figure ). an assembly size of 75.37 mb was obtained using mira assembler having 15281 contigs with n50 value of 26586 bp and largest contig length being 249590 bp. further this assembly was improved using cap3 software. finally, we obtained an assembly […]


Complete Genome Sequence of Lytic Bacteriophage VPUSM 8 against O1 El Tor Inaba Vibrio cholerae

PMCID: 5477385
PMID: 28546472
DOI: 10.1128/genomeA.00073-17

[…] (life technologies, inc.) at aitbiotech, singapore. sequence reads were processed on the ion torrent server to remove adapter sequences, and a quality score was assigned. reads were assembled in mimicking intelligent read assembly (mira) version 3.9.9 using the de novo method (, ). coding sequences (cdss) within the vpusm 8 genome were allocated using vector nti advance and cds finder […]


Genome Sequence of “Candidatus Carsonella ruddii” Strain BC, a Nutritional Endosymbiont of Bactericera cockerelli

PMCID: 5408110
PMID: 28450512
DOI: 10.1128/genomeA.00236-17

[…] reads, the contigs and scaffolds were filtered by g+c content and contig lengths. in order to complete the genome assembly, filtered reads and contigs were reassembled into gapped regions using mimicking intelligent read assembly (mira) version 4.0.2 (). the remaining gaps were closed using sanger sequencing of pcr products. the assembled genome was annotated using both the rapid annotation […]

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MIRA institution(s)
Department of Molecular Biophysics, German Cancer Research Centre Heidelberg, Heidelberg, Germany; MWG Biotech AG, Ebersberg, Germany; RZPD German Resource Center for Genome Research, Berlin, Germany; VitiGen AG, Siebeldingen, Germany; Abteilung Angewandte Molekularbiologie, Institut fur Physiologische Chemie, Universitat Mainz, Mainz, Germany; Institute for Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany

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