ERNE 2.1

Take advantage of an extensive set of tools designed to handle short reads by employing this extended randomized numerical aligner

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What's new in ERNE 2.1:

  • improved: erne-meth now uses compressed counters. Space in RAM reduced by approximately 4 times.
  • improved: optimized code of cw-bwt algorithm in the BWTIL library. Faster reference construction.
  • bugfix: removed elements in README, which caused problems in the html version of the manual
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LICENSE TYPE:
GPL 
FILE SIZE:
712 KB
USER RATING:
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DEVELOPED BY:
University of Udine
CATEGORY:
Home \ Math/Scientific
4 ERNE Screenshots:
ERNE - Help screen for the application when running it from a terminal window.ERNEERNEERNE
ERNE is an easy to use short string alignment application that provides a unique set of tools for handling short reads.

It has multiple components, including ERNE-MAP, ERNE-DMAP, ERNE- BS5 and ERNE-VISUAL.

ERNE is based on rNA, a sensitive and highly performing aligner for Illumina reads.

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.

Last updated on October 1st, 2014

Runs on: Mac OS X (-)

feature list

#numerical aligner #short read handler #sequence mapper #aligner #mapper #sequence #short read

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