Anne-Katrin Emde, David Weese, Marcel Schulz, Stefan Haas, and Knut Reinert
Bioinformatics, published online Jan 2012


NGS has a variety of applications, one of them being genome resequencing. Sequenced reads that contain structural variation compared to a reference genome may be hard to map by conventional mapping strategies. As a branch of our generic read mapper RazerS, we have developed a tool SplazerS for mapping reads containing structural variants, implemented in the highly efficient SeqAn C++ software library. SplazerS employs "split" read mapping, where prefix and suffix match of a read may be interrupted by a longer gap. This split read mapping is useful in the context of mRNA sequencing, where introns cause so-called junction reads that span exon-exon boundaries, or for the detection of small to medium-sized insertions and deletions in genomic data.

Main Features

  • supports split mapping on single end reads
  • supports anchored split mapping on paired end reads
  • configurable prefix and suffix match parameters
  • supports Hamming and edit distance read mapping with configurable error rates
  • reads can be of arbitrary length
  • supports SAM output format

SplazerS Binaries

Currently, the precompiled downloadable zip-folder contains a binary for Linux64. The source code can be accessed and compiled following the SeqAn Getting Started guidelines. Please take a look at the README file for usage instructions.

Version History

2011-04-27: v1.1

  • supports SAM input for anchored split mapping (currently only one chromosome at a time)
  • supports SAM output format
  • added precomputed parameter files for short minimum match lengths (10-14bp)
  • default minimum match length set to 18bp (previously 23bp in v1.0)

2010-12-22: v1.0

  • first release of SplazerS


For questions, comments, or suggestions feel free to contact Anne-Katrin Emde.


Last Update 4. March 2012