MIRA pipeline

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



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  • person_outline Bastien Chevreux <>

Publication for Mimicking Intelligent Read Assembly

MIRA citations

PMCID: 5809470

[…] and homopolymers (marinier et al., 2015). all reads that passed all filters were used in downstream analysis. draft genome assembly was performed using wgs assembler (myers et al., 2000) and mira (chevreux et al., 2004) for illumina miseq and ion torrent pgm reads, respectively., the bioinformatics program edgar (blom et al., 2009) was used to predict the pan-genome (gene repertoire), […]

PMCID: 5356052

[…] system) with an ion pgm hi-q view sequencing kit (thermo fisher scientific)., in total, 428,739 reads (mean length, 289 bases) generated 124 mb (114 mb with ≥q20) of data. reads were assembled using mira version 4.0rc4 (5), trimmed into 270 contigs ≥500 bp, giving a consensus length of 4,188,588 bp at 39.4× coverage (largest contig, 471,073 bp; n50, 139,640 bp). the genome sequence of b. lichenif […]

PMCID: 5214804

[…] on the length of each gene segment and sequenced using 454™ gs-flx pyrosequencing as previously described (heylen et al., 2015). obtained reads were mapped against g1p[8] reference strain wa using mira 3.4 (chevreux et al., 2004) and assemblies were visually inspected in tablet (milne et al., 2013). subsequently the consensus sequences for 9 gene segments of rotarix™ were determined, used […]

PMCID: 4213813

[…] as previously described using roche’s 454 technology [6]. accession numbers for the gypsy plains and dawn strains are: cp006846 and cp006847, respectively. raw 454 fastq files were mapped using mira v3.9.16 [33] using the st. maries genome as a backbone sequence. once the contigs were generated, the 454 reads were mapped to the assembled contigs. bovine sequences were then filtered […]

PMCID: 3045460

[…] to identify contigs which showed the most differential expression as these could potentially be associated with pyrethroid resistance. resistant and susceptible reads were separately assigned by mira to create contigs, assigned by tblastx (e = 10−3) to references of an. gambiae, ae. aegypti and an. funestus. these reads were normalized on the total number of susceptible or resistant reads. […]

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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