NGS plus plus : a library for rapid prototyping of epigenomics software tools
NGS plus plus : a library for rapid prototyping of epigenomics software tools
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DOI：
10.1093/bioinformatics/btt312
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发表时间：
2013-08-01
期刊：
影响因子：
5.8
通讯作者：
Gevry, Nicolas
中科院分区：
文献类型：
--
作者：
Markovits, Alexei Nordell;Beauparlant, Charles Joly;Gevry, Nicolas
动机：开发能够测试和分析高通量测序数据的计算工具对于现代基因组学研究至关重要。然而，尽管已经开发了多个框架来促进对这些工具的访问，但在实现低级编程库以提高其开发速度和简易性方面所做的努力相对较少。结果：我们提出了 NGS++，这是一个 C++11 编程库，专门用于操作下一代测序 (NGS) 数据集和基因组信息文件。该库可以轻松集成新格式并快速构建新功能原型，重点分析基因组区域和特征。它提供了一个强大、多功能且易于扩展的接口来读取、写入和操作多种基因组文件格式。通过标准化内部数据结构并为数据解析器提供通用接口，NGS++ 为表观基因组学工具开发提供了有效的框架。
Motivation: 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.Results: 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.