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.

Keywords: Perl; RNA-seq; next generation sequencing; pipelines; read mapping.

Figure 1.. Schematic overview of ViennaNGS components.

Core modules can be combined within a data analysis script in a flexible manner to meet individual analysis objectives and experimental setup.

Figure 2.. Class diagram illustrating the relations among generic Moose classes which are used as abstract representations of genomic intervals (only attributes are shown).

Figure 3.. Schematic representation of genomic interval classes in terms of their corresponding feature annotation.

Simple intervals (“features”) are characterized by ViennaNGS::Feature objects (bottom box). At the next level, ViennaNGS::FeatureChain bundles these, thereby maintaining individual annotation chains for e.g. UTRs, exons, introns, splice junctions, etc. (middle box). The topmost level is given by ViennaNGS::FeatureLine objects, representing individual transcripts.