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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


Complete genome sequence of native Bacillus cereus strains isolated from intestinal tract of the crab Ucides sp.

PMCID: 5723261
PMID: 29234696
DOI: 10.1016/j.dib.2017.11.049
call_split See protocol

[…] re removed using the fastq_quality_filter script from the fastx-toolkit package (http://hannonlab.cshl.edu/fastx_toolkit/). De novo genome assemblies were generated for each strain using MIRA (http://mira-assembler.sourceforge.net/), SPAdes and Newbler (http://www.roche.com/), and for each strain a consensus assembly was generated using CISA . The final set of contigs from each strain was ordered […]


Re Assembly and Analysis of an Ancient Variola Virus Genome

PMCID: 5618019
PMID: 28885569
DOI: 10.3390/v9090253

[…] d 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, when […]


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

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

[…] A 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 of si […]


Draft genome sequencing of the sugarcane hybrid SP80 3280

PMCID: 5499785
PMID: 28713559
DOI: 10.5256/f1000research.12814.r23398

[…] iridiplantae, resulting in 1,224,061 useful for assembly. Prior to assembly, long reads originating from mitochondria (NC_008360.1) and chloroplast (NC_005878.2) were excluded using mirabait ( http://mira-assembler.sourceforge.net/). Reads longer than 1.5Kbp were assembled using Celera’s WGS Assembler v8.2 , using similar parameters as previously described , except for some of the error parameters […]


Comparative genomic analysis between Corynebacterium pseudotuberculosis strains isolated from buffalo

PLoS One
PMCID: 5406005
PMID: 28445543
DOI: 10.1371/journal.pone.0176347

[…] genomes, unite them into a single scaffold, and establish the start of the chromosome. Simba includes three different assembly packages: SPAdes 3.6.0 []; MIRA 3.9.18 (http://sourceforge.net/projects/mira-assembler/); and Newbler 2.9 (http://swes.cals.arizona.edu/maier_lab/kartchner/documentation/index.php/home/docs/newbler). A “best” assembly was selected for each isolate based on having the high […]


Insights into the Psychrophilic and Sea Ice Specific Lifestyle of Marinobacter sp. Strain AC 23: a Genomic Approach

Genome Announc
PMCID: 5391408
PMID: 28408670
DOI: 10.1128/genomeA.00134-17
call_split See protocol

[…] bp chemistry on the Ion Torrent PGM platform (Life Technologies, Inc., USA). A total of 4,149,715 high-quality reads were generated upon sequencing of the genome. De novo assembly was performed using MIRA assembler version 4.0.5 (), resulting in 105 contigs. Functional annotation was performed using the Rapid Annotations using Subsystems Technology (RAST) server (). The RAST tool identified Marino […]


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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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