The ViennaNGS Perl distribution is available through CPAN at http://search.cpan.org/dist/Bio-ViennaNGS. The latest development release is available via the ViennaNGS Github repository.
ViennaNGS comes with extensive documentation and a Tutorial which guides prospective users through the first steps with the software. Input data required for running the tutorial scripts can be downloaded here:
Tutorial_pipeline00.pl: Inferring quantitative and qualitative parameters from an input BAM file.
Tutorial_pipeline01.pl: Computation and analysis of sequence motifs in close proximity to gene starts in a set of ENCODE human protein coding genes.
Tutorial_pipeline02.pl: Extraction and manipulation of strand-specific ENCODE RNA-seq data and automatic generation of coverage profiles.
Tutorial_pipeline03.pl: Automatic generation of UCSC genome browser Track Hubs for visualization of ENCODE RNA-seq data