WHAT IS SEQAN?

SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. Our library applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. SeqAn is easy to use and simplifies the development of new software tools with a minimal loss of performance.

DATA STRUCTURES

SeqAn offers many data structures for sequence analysis. For example a unified interface for searching in string indices or succinct data structures for pangenomics.

ALGORITHMS

SeqAn offer many core algorithms for sequence analysis. For example, pairwise and multiple alignments, approximate string searches and filter algorithms.

PARALLELIZATION

SeqAn support modern Hardware.
SIMD vectorization and multicore processing are being incorporated in core algorithmic components.

Input and Output

In times of large sequencing data fast I/O is crucial. Learn about SeqAn I/O modules and supported data formats.

APPS

Many efficient applications by different scientific groups and companies are based on SeqAn. Official applications by SeqAn project members are presented here and also some third party apps.

WORKFLOWS

Often several applications are connected in involved scientific workflows. SeqAn supports easy integration of its applications into workflows.

Center for Integrative Bioinformatics

SeqAn is partner of the Center for Integrative Bioinformatics (CIBI) in the de.NBI network and offers services for analysing sequencing data. Our services include the development and maintenance of the SeqAn library, its associated applications and the build and test infrastructure of them, as well as, training and education by organising regular developer and user meetings and providing online training materials.

Learn more about the CIBI center and its portfolio to find the best solution for your data and your type of project.

QUICK FACTS

Programming Language:

C++11/C++14

License:

3-clause-BSD[Free and Open Source]

UNIX Support:

(Linux, macOS & BSD)
· GCC ≥ 4.9
· Clang/LLVM ≥ 3.5
· ICC ≥ 16.0.2

Windows Support:

· Visual C++ ≥ 14 (Visual Studio 2015)
· ICC ≥ 16.0.2 (Visual Studio 2015u2)
· Clang/C2 ≥ 3.8.0 (Visual Studio 2015u2)

Recent News

January 23

SeqAn 3.0.1 released

We are excited to present a new update of our SeqAn lib …

Intel regards SeqAn as a very promising software package that has all the right ingredients to considerably speed up Next Generation Sequencing analysis on modern Intel processors. We are looking forward to collaborating with Professor Reinert and his team to add our technical know-how about Intel® Architecture and combine it with his algorithmic expertise, and in this way turn SeqAn into a premier software tool in this domain of rapidly growing importance.

Kristina Kermanshahche Chief Architect, Intel® Health & Life Sciences
Intel®

Recent Tweets

CITATIONS

If you publish software that uses SeqAn, please do not forget to cite:
K. Reinert, T. H. Dadi, M. Ehrhardt, H. Hauswedell, S. Mehringer, R. Rahn, J. Kim, C. Pockrandt, J. Winkler, E. Siragusa, G. Urgese, and D. Weese. The seqan c++ template library for efficient sequence analysis: a resource for programmers. Journal of biotechnology, vol. 261, pp. 157-168, 2017.

SeqAn Library

Efficient, robust code
SeqAn supports good software engineering practices like continuous integration and code reviews to maintain a high standard in its code base.

SeqAn Release 3.0.1

We just released the latest SeqAn. Look at the news for all changes and additions.