Applications

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

  @article{fu_mi_publications2103,
   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). Results 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. Conclusions 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. Keywords 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 = {http://publications.imp.fu-berlin.de/2103/},
   volume = {261},
   year = {2017}
  }

Official

• ANISE and BASIL - Breakpoint detection for structural variants ^SeqAn2

• Chopper - Optimizing the space consumption of a Hierarchical Binning Directory ^SeqAn3

• DFI - Sequential pattern mining ^SeqAn2

• DREAM-Stellar - A parallelized, updated version of the pairwise local aligner Stellar ^SeqAn3

• Fiona - A parallel and automatic strategy for read error correction ^SeqAn2

• Gustaf - A generic multi-split detection method ^SeqAn2

• JST - Journal string tree data structure and traverser ^SeqAn2

• LAMBDA - A local aligner optimized for many query sequences and searches in protein space ^SeqAn2

• LaRA 2 - Efficient sequence-structure alignments of ncRNA ^SeqAn2

• MaRs - Motif-based aligned RNA searcher ^SeqAn3

• Mason - A read simulator software for Illumina, 454 and Sanger reads ^SeqAn2

• Needle - A fast and space-efficient prefilter for estimating the quantification of very large collections of nucleotide sequences ^SeqAn3

• Rabema - a new read mapper benchmark methodology ^SeqAn2

• Raptor - A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences ^SeqAn3

• RazerS 3 - A read mapping program with adjustable sensitivity ^SeqAn2

• SeqAn::T-Coffee - A multiple sequence alignment program ^SeqAn2

• SeqCons2 - Consensus computation program ^SeqAn2

• SLIMM - Species level identification of microbes from metagenomes ^SeqAn2

• Stellar - A local pairwise aligner ^SeqAn2

• String Similarity Search/Join - Optimal string similarity search and join ^SeqAn2

• TetRex - Regular expression matching of biological motifs ^SeqAn3

• Vaquita - Fast and accurate identification of structural variation using combined evidence ^SeqAn2

• Yara - Yet another read aligner ^SeqAn2

Coming Soon

• iGenVar - An SV, indel, and SNP caller using short and long reads ^SeqAn3

Third-party

• Bowtie - A short read aligner

• Delly - Integrated structural variant discovery

• Flexbar - Flexible barcode and adapter removal

• Mitotool - Handling mtDNA sequence data

• Mugsy - A multiple whole genome aligner

• Popins - Population-scale detection of novel-sequence insertions

• Tophat - A spliced read mapper for RNA-Seq