SeqAn

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Application data

Created by Knut Reinert, Andreas Gogol-Döring, David Weese, Tobias Rausch, Anne-Katrin Emde, Birte Kehr, Marcel Schulz, Manuel Holtgrewe
Biological application domain(s) Sequence analysis, Genomics, Phylogenetics
Principal bioinformatics method(s) Algorithms and datastructures for the Bioinformatics toolbox.
Technology Sanger, Solexa, 454
Created at Free University of Berlin
Maintained? Yes
Input format(s) FASTA, FASTQ, SAM, GFF
Output format(s) FASTA, FASTQ, SAM, GFF
Programming language(s) C++
Licence BSD License (3-clause)
Operating system(s) UNIX and Windows

Summary: C++ template library with many sequence analysis algorithms and datastructures. 200px|right

"Error: no local variable "counter" was set." is not a number.

Description

SeqAn is a C++ template library of efficient biological sequence analysis data structures and algorithms. The main aims are performance, extensibility, ease of use, and portability. It is the basis for the tools of the Reinert lab at Free University of Berlin. Illumina's latest Casava software uses SeqAn functionality.

Contents Include:

  • Various efficient string representation and alphabets.
  • Index datastructures (e.g. q-gram index, extended suffix arrays) and algorithms for them.
  • Online string search algorithms.
  • String filter algorithms (SWIFT, Quasar).
  • Graph data structures and algorithms.
  • Efficient implementations of alignment data structures and algorithms.
  • Data structure for the efficient handling of NGS data and annotations (FragmentStore).
  • Random number generation

Additional Links

Supported Compilers

  • GCC 4.x
  • LLVM (current trunk)
  • Visual Studio 2005, 2008, 2010

Links


References

  1. . 2008. BMC Bioinformatics


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