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

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

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

Abstract
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.

Availability: 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.

Related Links (Giithub):

NGSplusplus   https://github.com/jameslz/NGSplusplus
NGSplusplus-Examples   https://github.com/NGS-lib/NGSplusplus-Examples
PythonWrapping   https://github.com/NGS-lib/PythonWrapping

Related Preject:
  1. SeqAn ,  An efficient, generic C++ library for sequence analysis.   http://www.seqan.de/
  2. Bio++ ,  A set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics. http://biopp.univ-montp2.fr/
  3. NCBI Tools++ , ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/
  4. libStatGen , Useful set of classes for creating statistical genetic programs.  http://genome.sph.umich.edu/wiki/C%2B%2B_Library:_libStatGen
  5. GenomicTools , a computational platform for developing high-throughput analytics in genomics.  http://code.google.com/p/ibm-cbc-genomic-tools/
  6. MolBioLib , A C++11 Framework for Rapid Development and Deployment of Bioinformatics Tasks.  http://sourceforge.net/projects/molbiolib/
  7. libsleipnir The Sleipnir library for computational functional genomics.  http://libsleipnir.bitbucket.org/
  8. libsequence ,  A C++ class library for evolutionary genetic analysis.  http://molpopgen.org/software/libsequence.html
Read More:
BioStar , Question: C/C++ libraries for bioinformatics?   http://www.biostars.org/p/1515/
欢迎大家添加新的生物信息学C++库。

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