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

Wolfinger MT, Fallmann J, Eggenhofer F, Amman F - F1000Res (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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.

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.

No MeSH data available.


Schematic overview ofViennaNGS components.Core modules can be combined within a data analysis script in a flexible manner to meet individual analysis objectives and experimental setup.
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f1: Schematic overview ofViennaNGS components.Core modules can be combined within a data analysis script in a flexible manner to meet individual analysis objectives and experimental setup.

Mentions: The major design consideration for theViennaNGS toolbox was to make available modular and reuseable code for NGS processing in a popular scripting language. We therefore implemented thematically related functionality in different Perl modules under theBio namespace (Figure 1).


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

Wolfinger MT, Fallmann J, Eggenhofer F, Amman F - F1000Res (2015)

Schematic overview ofViennaNGS components.Core modules can be combined within a data analysis script in a flexible manner to meet individual analysis objectives and experimental setup.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4513691&req=5

f1: Schematic overview ofViennaNGS components.Core modules can be combined within a data analysis script in a flexible manner to meet individual analysis objectives and experimental setup.
Mentions: The major design consideration for theViennaNGS toolbox was to make available modular and reuseable code for NGS processing in a popular scripting language. We therefore implemented thematically related functionality in different Perl modules under theBio namespace (Figure 1).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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.

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.

No MeSH data available.