MIRA protocols

MIRA computational protocol

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 IN pipelines

PMCID: 5809470
PMID: 29472910
DOI: 10.3389/fmicb.2018.00161

[…] 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: 5214804
PMID: 28070453
DOI: 10.7717/peerj.2733

[…] 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: 5421314
PMID: 28453770
DOI: 10.1093/gbe/evx086

[…] derived from food prokaryotes as described in harding et al. (2016)., genomic contigs for bb2 and p. kirbyi were assembled with the de novo assemblers ray v2.3.1 (boisvert et al. 2010) and/or mira v4.9.5_2 (chevreux et al. 2004). for p. kirbyi, a second round of decontamination was performed by using assembled contig sequences as queries in blastn searches against the nt database. […]

PMCID: 5656758
PMID: 28809152
DOI: 10.1099/jgv.0.000880

[…] center, university of illinois at urbana-champaign). sequences were assembled de novo using the ray assembler program (ray version 2.3.1, publicly available software) [36] and for mapping assembly mira version 4 was used [37]. in all cases, assembly of the next-generation data produced a single contiguous sequence of the expected size. these were examined using tablet [38] for quality, snp […]

PMCID: 5678564
PMID: 29115952
DOI: 10.1186/s12917-017-1239-5

[…] system using the 200-bp read chemistry and an ion 316 chip. this was performed as described earlier [33] at the uppsala genome center, scilifelab, sweden. the resulting reads were assembled using mira [34] with the standard settings for de novo assembly of ion torrent data. taxonomic classification of assembled contigs was enabled by blastn and blastx searches against local copies of ncbi’s […]

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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