The MIRO pipeline - Analysis of microRNAs using short-read deep sequencing data.


The MIRO (the miRNA omics) pipeline is a flexible and powerful tool for the analysis of miRNA (or more generall short RNA) expression using short-read deep sequencing data. In its present implementation MIRO is especially adapted for the analysis of reads generated with the Illumina sequencing platform. MIRO allows to preprocess the Solexa-reads, map them flexibly to several reference genomes using one of four different mappers, create differential gene (miRNA) expression profiles and cluster reads using one of several algorithm. MIRO output is furthermore compatible with software such as genome browsers and miRDeep.


Download MIRO release candidate 2.9


The MIRO documentation


Miro is available free for academic use. For a commercial licence please contact: heinz.himmelbauer at

In any case please cite:

Robert Kofler, Manuela Hummel, Juliane Dohm, Matthew Ingham, Lauro Sumoy and Heinz Himmelbauer (2009), MIRO: Analysis of microRNAs using short-read deep-sequencing data; submitted



Dowload the current MIRO release


Unpack the file in the folder of your choosing


Edit the file log/pipelog_config.txt and set the path to the MIRO log files. This step is optional. An error message will however be issued if the log files have not been provided


Install the necessary prerequisites. Each MIRO script has individual prerequisites (mainly R 2.7.0) which will be mentioned in the documentatin

For the full functionallity of MIRO you need:

Perl 5.8 or higher

R 2.7.0 or higher

R-library geneplotter

R-library gplots

WebLogo 3.0


One of the following mappers: Eland, SeqMap, SOAP, Gem


Start by using the script See the documentation for this script.

Test data

We used the publicly available data published by Glazov et al. (2008) to test the MIRO pipeline. The results of this example run are available as supplementary file S2 in the publication. If you want to test MIRO please use this data and compare your results with the results published in supplementary file S2. The test data can be obtained at:

The test data set

Glazov EA, Cottee PA, Barris WC, Moore RJ et al. A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res 2008 Jun;18(6):957-64. PMID: 18469162


Please report bugs to the email address shown below!

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heinz.himmelbauer at