We present ERNE (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 comprises ERNE-FILTER (read trimming and continamination filtering), ERNE-MAP (core alignment tool/algorithm), ERNE-BS5 (bisulfite treated reads aligner), and ERNE-PMAP/ERNE-PBS5 (distributed versions of the aligners),
The ERNE aligner is easy to install, extremely fast (maybe the fastest aligner in the world in ungapped scenarios) and precise. Also ERNE-filter, the trimming algorithm, is the fastest of the bunch out there.