ERNE - Extended Randomized Numerical alignEr

Welcome to ERNE 2!

The Extended Randomized Numerical alignEr using BWT

We present ERNE 2 (Extended Randomized Numerical alignEr), a short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads. ERNE 2 (a.k.a. bw-erne) uses the Burrows Wheeler Transformation (BWT) to reduce memory requirements preserving its speed and accuray. ERNE 2 comprises ERNE-MAP (core alignment tool/algorithm), ERNE-BS5 (bisulfite treated reads aligner), ERNE-FILTER (quality trimming and contamination filtering), and parallel version of the aligners (ERNE-PMAP and ERNE-PBS5). The alignment core supports indels and one long gap.

ERNE is based on rNA (randomized Numerical Aligner)

rNA is an highly performing and sensitive aligner for Illumina reads. We have improved the rNA core algorithm and added several new freatures.

ERNE and rNA were developed at Istituto di Genomica Applicata and at University of Udine.


Available software in ERNE 2 package are:

  • ERNE-MAP: align short DNA or RNA reads against a genome;
  • ERNE-BS5: align short reads treated with bisulfite against a genome;
  • ERNE-CREATE: preprocess a reference file to be used with ERNE-MAP and ERNE-BS5;
  • ERNE-FILTER: does quality trimming and contamination filtering;
  • ERNE-PMAP,ERNE-PBS5,ERNE-PCREATE: parallel versions to be used in a cluster of computer (EXPERIMENTAL)


  • Works in GNU/Linux, OSX, and Windows(tm) environments;
  • Fast and accurate mapping;
  • Succint data structure (using BWT);
  • Indels searching;
  • Long gap support;
  • Both single and paired ends reads support;
  • DNA-seq, RNA-seq, and BS-seq ready;
  • Multithreading;
  • MPI-enabled;
  • Automatic trimming using FASTQ quality;
  • Automatic FASTQ version detection;


  • A Parallel Algorithm for the Best k-mismatches Alignment Problem
    Del Fabbro C., Tardivo F., and Policriti A.
    Proceedings of 2014 22nd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing (PDP2014), Turin, Italy, February 12-14, 2014, 0:586-589 doi:10.1109/PDP.2014.51
  • ERNE-BS5: Aligning BS-treated Sequences by Multiple Hits on a 5-letters Alphabet
    Prezza N., Del Fabbro C., Vezzi F., De Paoli E., and Policriti A.
    Proceedings of The 2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB 2012), Orlando (Florida), U.S.A., October 7-10, 2012, Association for Computing Machinery, 0:12-19, ISBN: 978-1-4503-1670-5, doi:10.1145/2382936.2382938
  • rNA: a Fast and Accurate Short Reads Numerical Aligner
    Vezzi F., Del Fabbro C., Tomescu A.I., and Policriti A.
    Bioinformatics, Vol.28, Issue 1, January 2012, pp. 123-124, doi:10.1093/bioinformatics/btr617
  • 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) U.S.A., November 12-15, 2011, IEEE Computer Society 0:139-142, ISBN 978-0-7695-4574-5doi:10.1109/BIBM.2011.17

If you use ERNE-FILTER, please cite:

  • An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis
    Del Fabbro C., Scalabrin S., Morgante M., Giorgi F.M.
    PlosOne, December 23, 2013, Vol. 8(12):e85024, doi:10.1371/journal.pone.0085024

Latest News

Udated on December 20, 2013

  • September 29, 2014: Released major version 2.0 with a new data structure based on BWT.
  • January 30, 2014: Released minor version 1.4.2 with better code stability.
  • December 20, 2013: Released minor version 1.4.1 for a bugfix in erne-filter.
  • December 16, 2013: Released version 1.4 with a reimplementation for a better integration with parallel version.
  • June 13, 2012: First implementation, forked from rNA;