NGS++: a library for rapid prototyping of epigenomics software tools

• Published in: Bioinformatics 2013-08, Vol.29 (15), p.1893-1894
• Main Authors: Nordell Markovits, Alexei, Joly Beauparlant, Charles, Toupin, Dominique, Wang, Shengrui, Droit, Arnaud, Gevry, Nicolas
• Format: Article
• Language: English
• Subjects: Computer programs; Construction; Documentation; Epigenomics - methods; Format; High-Throughput Nucleotide Sequencing; Libraries; Programming; Rapid prototyping; Software; Source code
• ISSN: 1367-4803; 1367-4811; 1460-2059
• DOI: 10.1093/bioinformatics/btt312

The development of computational tools to enable testing and analysis of high-throughput-sequencing data is essential to modern genomics research. However, although multiple frameworks have been developed to facilitate access to these tools, comparatively little effort has been made at implementing low-level programming libraries to increase the speed and ease of their development. We propose NGS++, a programming library in C++11 specialized in manipulating both next-generation sequencing (NGS) datasets and genomic information files. This library allows easy integration of new formats and rapid prototyping of new functionalities with a focus on the analysis of genomic regions and features. It offers a powerful, yet versatile and easily extensible interface to read, write and manipulate multiple genomic file formats. By standardizing the internal data structures and presenting a common interface to the data parser, NGS++ offers an effective framework for epigenomics tool development. NGS++ was written in C++ using the C++11 standard. It requires minimal efforts to build and is well-documented via a complete docXygen guide, online documentation and tutorials. Source code, tests, code examples and documentation are available via the website at http://www.ngsplusplus.ca and the github repository at https://github.com/NGS-lib/NGSplusplus. [e-mail] or [e-mail].