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.
rNA is an highly performing and sensitive aligner for Illumina reads. We have improved the rNA core algorithm and added several new freatures.
Available software in ERNE 2 package are:
If you use ERNE-FILTER, please cite:
Udated on December 20, 2013