Bio::ViennaNGS - A Perl distribution for Next-Generation Sequencing (NGS) data analysis
Bio::ViennaNGS is a distribution of Perl modules and utilities for building efficient Next-Generation Sequencing (NGS) analysis pipelines. It covers various aspects of NGS data analysis, including (but not limited to) conversion of sequence annotation, evaluation of mapped data, expression quantification and visualization.
The main Bio::ViennaNGS module is shipped with a complementary set of (sub)modules:
Bio::ViennaNGS comes with a collection of command line utilities for accomplishing routine tasks often required in NGS data processing. These utilities serve as reference implementation of the routines implemented throughout the modules and can readily be used for atomic tasks in NGS data processing:
The Bio::ViennaNGS modules and classes depend on a set of Perl modules, some of which are part of the Perl core distribution, most notably Bio::Perl >= 1.00690001 and Bio::DB::Sam >= 1.37.
In addition, Bio::ViennaNGS depends on third-party tools and libraries which are required for specific filtering and file format conversion tasks as well as for building internally used Perl modules:
Please ensure that all third-party utilities are available on your system, and that hey can be found and executed by the Perl interpreter.
Source code for this distribution is available from the ViennaNGS Github repository.
A pre-compiled binary distribution for Linux and MacOS is available from Bioconda, e.g. via conda install perl-bio-viennangs.
If the Bio::ViennaNGS suite is useful for your work or if you use any component of the distribution in a custom pipeline, please cite the following publication:
"ViennaNGS - A toolbox for building efficient next-generation
sequencing analysis pipelines"
Michael T. Wolfinger, Joerg Fallmann, Florian Eggenhofer and Fabian
Amman; F1000Research (2015), 4:50
The Bio::ViennaNGS suite is actively developed and tested on different flavours of Linux and Mac OS X. We have taken care of writing platform-independent code that should run out of the box on most UNIX-based systems, however we do not have access to machines running Microsoft Windows. As such, we have not tested and will not test Windows compatibility.
Copyright (C) 2014-2018 Michael T. Wolfinger <email@example.com>
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.10.0 or, at your option, any later version of Perl 5 you may have available.
This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
To install Bio::ViennaNGS, copy and paste the appropriate command in to your terminal.
perl -MCPAN -e shell
For more information on module installation, please visit the detailed CPAN module installation guide.