ViennaNGS

ViennaNGS is a collection of Perl modules designed to help researchers build efficient pipelines for processing next-generation sequencing (NGS) data. It includes features for extracting and converting data from common NGS file formats, computing and evaluating read mapping statistics, and normalizing RNA abundance. Additionally, ViennaNGS provides software components for identifying and characterizing splice junctions from RNA-seq data, parsing and condensing sequence motif data, and automating the construction of Assembly and Track Hubs for the UCSC genome browser. The tool also includes wrapper routines for commonly used NGS command line tools. ViennaNGS is intended to simplify the compilation of customized analysis workflows for big genomics data.

Topic

RNA-seq;Workflows;ChIP-seq

Detail

  • Operation: Standardisation and normalisation;RNA-Seq quantification;Expression analysis;Read mapping

  • Software interface: Command-line user interface

  • Language: Perl

  • License: -

  • Cost: Free

  • Version name: 0.19.2

  • Credit: Austrian Science Fund, the Research Platform “Decoding mRNA decay in inflammation” by the University of Vienna.

  • Input: -

  • Output: -

  • Contact: florian.eggenhofer@univie.ac.at;fabian@tbi.univie.ac.at;michael@wolfinger.eu;fall@tbi.univie.ac.at

  • Collection: -

  • Maturity: -

Publications

  • ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines.
  • Wolfinger MT, et al. ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines. ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines. 2015; 4:50. doi: 10.12688/f1000research.6157.2
  • https://doi.org/10.12688/f1000research.6157.2
  • PMID: 26236465
  • PMC: PMC4513691

Download and documentation

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