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The SeqAn C++ template library for efficient sequence analysis: A resource for programmers.

Knut Reinert1, Temesgen Hailemariam Dadi1, Marcel Ehrhardt1

  • 1Algorithmic Bioinformatics, Institute for Bioinformatics, FU Berlin, Takustrasse 9, 14195 Berlin, Germany.

Journal of Biotechnology
|September 11, 2017
PubMed
Summary
This summary is machine-generated.

The SeqAn library provides efficient bioinformatics tools for life science research, addressing the gap between advanced algorithms and practical applications. It continues to evolve, now supporting hardware acceleration for enhanced sequence analysis.

Keywords:
C++Data structuresNGS analysisSoftware libraries

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Life Sciences

Background:

  • Algorithmic techniques are crucial for life science problems like genome sequencing and next-generation sequencing (NGS) analysis.
  • A gap exists between state-of-the-art algorithms and widely used bioinformatics tools.
  • The SeqAn library was introduced in 2008 to provide efficient data types and algorithms for sequence analysis.

Purpose of the Study:

  • To review the status and contributions of the SeqAn library.
  • To highlight its maturation over 9 years as an established resource.
  • To discuss its role in various analysis tools.

Main Methods:

  • Review of the SeqAn library's development and features.
  • Analysis of its integration into bioinformatics tools.
  • Assessment of its impact on sequence analysis.

Main Results:

  • SeqAn has matured significantly since its initial publication.
  • It serves as an established resource for bioinformatics programmers.
  • The library has contributed to numerous analysis tools.

Conclusions:

  • SeqAn is expected to remain a valuable resource for bioinformatics.
  • Active support for hardware acceleration techniques is a key future direction.
  • Continued development will enhance its utility in sequence analysis.