ERNE 2.1.1 – Extended Randomized Numerical alignEr

ERNE 2.1.1

:: DESCRIPTION

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).

::DEVELOPER

Istituto di Genomica Applicata

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

 ERNE

:: MORE INFORMATION

Citation

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

rNA 1.0 / mrNA 1.0 / grNA 0.9 – randomized Numerical Aligner

rNA 1.0 / mrNA 1.0 / grNA 0.9

:: DESCRIPTION

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.

mrNA is the MPI version of the original rNA program.

grNA is a graphical front-end for rNA

::DEVELOPER

bioinformatics team at Istituto di Genomica Applicata (Applied Genomics Institute) andDepartment of Mathematics and Informatics, University of Udine.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

  rNA / mrNA / grNA

:: MORE INFORMATION

Citation

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

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