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MIRA specifications

Information


Unique identifier OMICS_00023
Name MIRA
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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Maintainer


  • person_outline Bastien Chevreux <>

Publication for Mimicking Intelligent Read Assembly

MIRA in pipelines

 (6)
2017
PMCID: 5371800
PMID: 28300778
DOI: 10.3390/v9030045

[…] used as verified by nanodrop quantification. confirmatory molecular id tests were also conducted on the dna extract prior to shipment to the sequencing facility (genprobio, parma, italy). the mira (mimicking intelligent read assembly) software program (version 4.0.2) [] was used for de novo assembly of miseq-derived phage genome sequences to generate a consensus sequence. quality improvement […]

2015
PMCID: 4972785
PMID: 26564050
DOI: 10.1128/genomeA.01336-15

[…] ca). in total, 1,135,644 reads with an average read length of 262 bp were obtained, which yielded 235 mb of total sequenced bases with 71-fold coverage. the de novo assembly was performed using mimicking intelligent read assembly (mira) version 3.9.18 (), which yielded 25 contigs. the largest contig was 444,937 bp long. the draft genome sequence of the b. abortus s19δper mutant […]

2014
PMCID: 3961413
PMID: 24651535
DOI: 10.1371/journal.pone.0092663

[…] was soft-masked using segmasker included as part of the blast+ distribution (version 2.2.25) . the code of stm was modified to allow dna ambiguity codes other than “n” in contigs as produced by the mira assembler., in order to assess completeness of the transcriptome assembly, the cegma pipeline (version 2.4) was used. additionally, est2assembly (version 1.13) was employed to compare […]

2013
PMCID: 3784788
PMID: 24072868
DOI: 10.1128/genomeA.00770-13

[…] reads with an average read length of 115 bp were obtained, which yielded 213.1 mb sequenced bases (~85-fold coverage of an ~2.5-mb genome). reference-based assembly was performed using mira (mimicking intelligent read assembly) version 3.9.17 with l. ferrmentum ifo 3956 (nc_010610) as the reference genome (). a total of 109 contigs were obtained and the total consensus was 2,566,297 bp […]

2013
PMCID: 4053977
PMID: 23800085
DOI: 10.1186/gb-2013-14-6-r66

[…] polyploid transcriptome assembly is the separation of homologs. the approach followed by schreiber et al. (2012), that implemented a computationally-intensive two-stage assembly using the stringent mira assembler in the last step, reduced the proportion of chimeric contigs to 18% and represented a step in the right direction[]. thepost-assembly read phasing pipeline presented in this study […]


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MIRA in publications

 (52)
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 […]

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 […]

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, […]

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 […]

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 […]


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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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