SeqAn
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Application data |
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| Created by | Reinert K, Gogol-Döring A, Weese D, Rausch T, Emde AK, Kehr B, Schulz M, Holtgrewe M |
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| Biological application domain(s) | Sequence analysis, Genomics, Phylogenetics |
| Principal bioinformatics method(s) | |
| Technology | Sanger, Illumina, 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 (3-clause) |
| Operating system(s) | UNIX, Mac OS X, Windows |
Summary: C++ template library with many sequence analysis algorithms and datastructures.
"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.
Supported Compilers
- GCC 4.x
- LLVM (current trunk)
- Visual Studio 2005, 2008, 2010
Additional Links
- SeqAn Tutorial (start here)
- Nightly API documentation
- Release API documentation
- SeqAn How To
- SeqAn Trac Wiki
Links
- SeqAn Mailing list [ edit link ]
- SeqAn Homepage [ edit link ]
- [ SeqAn ] [ edit link ]
- [ SeqAn ] [ edit link ]
- [ SeqAn ] [ edit link ]
- SeqAn Source code [ edit link ]
References
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