While ViennaNGS is not an established pipeline per se, it provides tools and functionality for the development of custom NGS pipelines in Perl. ViennaNGS comes with a set of utility scripts that serve as reference implementation for most library functions and can readily be applied for specific tasks or integrated as-is into custom pipelines.
ViennaNGS covers a broad range of NGS data processing tasks, including functionality for extracting and converting features from common NGS file formats, computation and evaluation of read mapping statistics, quantification and normalization of read count data, identification and characterization of splice junctions from RNA-seq data, parsing and condensing sequence motif data, automated construction of Assembly and Track Hubs for the UCSC genome browser and wrapper routines for a set of commonly used NGS command line tools.
ViennaNGS: A toolbox for building efficient next-generation sequencing analysis pipelines
Michael T. Wolfinger, Jörg Fallmann, Florian Eggenhofer, Fabian Amman
F1000Research 4:50 (2015) | doi: 10.12688/f1000research.6157.2 | PDF