ViennaNGS – A toolbox for building efficient next- generation sequencing analysis pipelines

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. Researchers at the University of Vienna 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.

rna-seq

Availability – The ViennaNGS distribution is available through the Comprehensive Perl Architecture Network (CPAN) and at GitHub. http://search.cpan.org/dist/Bio-ViennaNGS or  https://github.com/mtw/Bio-ViennaNGS

Wolfinger MT, Fallmann J, Eggenhofer F, Amman F. (2015) ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines. Version 2. F1000Res 4:50. [article]

Leave a Reply

Your email address will not be published. Required fields are marked *

*

Time limit is exhausted. Please reload CAPTCHA.