SeqAn is the foundation of many modern bioinformatics applications. Some of them are developed by the SeqAn team, mostly at Freie Universität Berlin. These are listed as Official Applications on the bottom. The downloads for most official apps, including some older (not listed) ones, can be found at the central SeqAn package repository.

Through our developer channels we know that many scientific groups and companies are using SeqAn for developing public and internal tools, among them Steven Salzberg’s team, PacBio, the Max-Planck-Institute for molecular Genetics and the Charite university hospital. A selection of these applications is listed as “Third-Party Applications” below.

The permissive open source BSD-license of the library enables you to integrate SeqAn into your applications with proper attribution being the only legal requirement. But, please also cite our most recent SeqAn publication when you use SeqAn in your academic work.

  • Knut Reinert, Temesgen Hailemariam Dadi, Marcel Ehrhardt, Hannes Hauswedell, Svenja Mehringer, René Rahn, Jongkyu Kim, Christopher Pockrandt, Jörg Winkler, Enrico Siragusa, Gianvito Urgese, David Weese, “The SeqAn C++ template library for efficient sequence analysis: A resource for programmers”, vol. 261, 2017-11-10.
    cite this publication
     abstract = {Background
    The use of novel algorithmic techniques is pivotal to many important problems in life science. For example the sequencing of the human genome (Venter et al., 2001) would not have been possible without advanced assembly algorithms and the development of practical BWT based read mappers have been instrumental for NGS analysis. However, owing to the high speed of technological progress and the urgent need for bioinformatics tools, there was a widening gap between state-of-the-art algorithmic techniques and the actual algorithmic components of tools that are in widespread use. We previously addressed this by introducing the SeqAn library of efficient data types and algorithms in 2008 (D{\"o}ring et al., 2008).
    The SeqAn library has matured considerably since its first publication 9 years ago. In this article we review its status as an established resource for programmers in the field of sequence analysis and its contributions to many analysis tools.
    We anticipate that SeqAn will continue to be a valuable resource, especially since it started to actively support various hardware acceleration techniques in a systematic manner.
    NGS analysis; Software libraries; C++; Data structures},
     author = {Knut Reinert and Temesgen Hailemariam Dadi and Marcel Ehrhardt and Hannes Hauswedell and Svenja Mehringer and Ren{\'e} Rahn and Jongkyu Kim and Christopher Pockrandt and J{\"o}rg Winkler and Enrico Siragusa and Gianvito Urgese and David Weese},
     journal = {Journal of Biotechnology},
     keywords = {NGS analysis; Software libraries; C++; Data structures},
     month = {November},
     pages = {157--168},
     publisher = {ELSEVIER},
     title = {The SeqAn C++ template library for efficient sequence analysis: A resource for programmers},
     url = {},
     volume = {261},
     year = {2017}


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