rNA (randomized Numerical Aligner) is a software able to align the huge amount of data produced by Next Generation Sequencers. The main feature of rNA is the fact that it achieves an accuracy greater than the majority of other tools in a feasible amount of time. rNA works with single as well as paired ends reads and it allows indels and delta-search for better accuracy. A graphical user interface is provided for not command-line-skilled users and an MPI-based version for cluster is in development.

rNA was developed by bioinformatics team at Istituto di Genomica Applicata (Applied Genomics Institute) and Department of Mathematics and Informatics, University of Udine.

rNA is no more manutenuted! We developed a more improved version and renamed to ERNE. Please go to the new home page


  • Works in GNU/Linux, OSX, and Windows(tm) environments
  • Fast and accurate mapping
  • Both single and paired ends reads support
  • Multithreading
  • MPI-enabled (under development)
  • Automatic trimming using FASTQ quality
  • Automatic FASTQ version detection
  • Indels search
  • Delta-alignment repeatition classification
  • Graphical User Interface through grNA java application

If you use rNA, please cite:
  • rNA: a Fast and Accurate Short Reads Numerical Aligner
    Vezzi F., Del Fabbro C., Tomescu A.I., and Policriti A.
    Bioinformatics, 2011, doi:10.1093/bioinformatics/btr617

If you use mrNA, please cite:
  • mrNA: the MPI randomized Numerical Aligner
    Del Fabbro C., Vezzi F., and Policriti A.
    Proceedings of 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), Atlanta (Georgia), November 12-15, 2011, IEEE Computer Society 0:139-142, ISBN 978-0-7695-4574-5

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If you need to contact us directly, send an email to
rna-support (at) appliedgenomics (dot) org