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Extended Randomized Numerical alignEr ERNE

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.

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ERNE classification

ERNE specifications

Software type:
Package/Module
Restrictions to use:
None
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 2.0
Version:
2.0
Maintained:
Yes
Interface:
Command line interface
Biological technology:
Illumina
Programming languages:
C++
Computer skills:
Advanced
Stability:
Stable

ERNE distribution

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Credits

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Publications

Institution(s)

Department of Mathematics and Computer Science, University of Udine, Udine, Italy

Link to literature

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