title: ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines.
abstract: Recent achievements in next-generation sequencing (NGS) technologies lead to a high demand for reuseable software components to easily compile customized analysis workflows for big genomics data. We present ViennaNGS, an integrated collection of Perl modules focused on building efficient pipelines for NGS data processing. It comes with functionality for extracting and converting features from common NGS file formats, computation and evaluation of read mapping statistics, as well as normalization of RNA abundance. Moreover, ViennaNGS provides software components for 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, as well as wrapper routines for a set of commonly used NGS command line tools.
authors.affiliation: Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090, Vienna, Austria ; Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria ; Department of Biochemistry and Molecular Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria.
authors.forename: Michael T
authors.initials: MT
authors.lastname: Wolfinger
authors.affiliation: Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090, Vienna, Austria.
authors.forename: Jörg
authors.initials: J
authors.lastname: Fallmann
authors.affiliation: Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090, Vienna, Austria.
authors.forename: Florian
authors.initials: F
authors.lastname: Eggenhofer
authors.affiliation: Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090, Vienna, Austria ; Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria.
authors.forename: Fabian
authors.initials: F
authors.lastname: Amman
keywords: Perl; RNA-seq; next generation sequencing; pipelines; read mapping