ERNE 2.1 – Extended Randomized Numerical alignEr

ERNE 2.1


ERNE is a short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads. ERNE comprises ERNE-MAP (align short DNA or RNA reads against a genome), ERNE-DMAP (distributed version of the aligner), ERNE- BS5 (align short reads treated with bisulfite against a genome), ERNE-FILTER (is a quality trimming and contamination filter for de novo assembly but can be used for alignments too), and ERNE-VISUAL (graphical user interface).


Istituto di Genomica Applicata and at University of Udine.




  • Linux / Windows / MacOsX





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

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