miRDeep2

Discovering known and novel miRNAs from deep sequencing data

 

 

Developed by Sebastian Mackowiak, Marc Friedländer and Nikolaus Rajewsky
Systems Biology group at the Max Delbrück Center, Berlin-Buch
April 20th, 2011

 

miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs. The tool reports known and hundreds of novel microRNAs with high accuracy in seven species representing the major animal clades. The low consumption of time and memory combined with user-friendly interactive graphic output makes miRDeep2 accessible for straightforward application in current reasearch.

 

Download: miRDeep2.0.0.8 (Latest Update: May 2016) contains the core algorithm script and all auxiliary scripts. Documentation.

The package is freely available for non-commercial purposes. For commercial purposes, please contact us.

 

For general comments or questions on commercial use, contact: rajewsky at mdc-berlin dot de.

Disclaimer

The miRDeep2 software package is provided as is without any guarantees or warranty for correctness. The authors are not responsible for any damage or loss of any kind caused by the use or misuse of the scripts included in the software package. The authors are not under obligation to provide support, service, corrections, or upgrades to the package.

 

miRDeep

Developed by Marc Friedländer and Nikolaus Rajewsky
Systems Biology group at the Max Delbrück Center, Berlin-Buch
April 4th, 2008

The miRDeep package was developed to discover active known or novel miRNAs from deep sequencing data (Solexa/Illumina, 454, ...). The package consists of everything you need to analyze your own deep sequencing data after removal of ligation adapters: a number of scripts to preprocess the mapped data, and the core miRDeep algorithm that will analyze and score these data.

 

The package is freely available for non-commercial purposes. For commercial purposes, please contact us.

 

If you use miRDeep in your scientific research, please cite us:

Friedländer, M.R., Chen, W., Adamidi, C., Maaskola, J., Einspanier, R., Knespel, S., Rajewsky, N. 'Discovering microRNAs from deep sequencing data using miRDeep', Nature Biotechnology, 26, 407-415 (2008)

 

Three compressed downloads are available at this site:

Both demo_limited and demo_full contain a README file that contains instructions how to run miRDeep on your own deep sequencing data. Running it on the demo data allows you to test that it produces what it is supposed to produce (positive control). We highly recommend to test the package on the demo data.

  1. miRDeep.tgz contains the core algorithm script and all auxiliary scripts.
  2. demo_limited.tgz contains all the files that we used to predict C. elegans known and novel miRNA, starting with the file containing the alignments of the filtered reads to the nematode genome and ending with the file of the final predictions (size of this demo: a few MB)
  3. demo_full.tgz contains all the files that we used to predict C. elegans known and novel miRNA, starting with the file containing the alignments of all reads to the nematode genome and ending with the file of the final predictions (warning: size of this file: 100 MB)

 

For general comments or questions on commercial use, contact: rajewsky at mdc-berlin dot de

(substitute 'at' with '@' and 'dot' with '.' to get the proper email addresses)