title: RazerS 3: faster, fully sensitive read mapping.
abstract: BACKGROUND
  During the past years, next-generation sequencing has become a key technology for many applications in the biomedical sciences. Throughput continues to increase and new protocols provide longer reads than currently available. In almost all applications, read mapping is a first step. Hence, it is crucial to have algorithms and implementations that perform fast, with high sensitivity, and are able to deal with long reads and a large absolute number of insertions and deletions.
  
  
  RESULTS
  RazerS is a read mapping program with adjustable sensitivity based on counting q-grams. In this work, we propose the successor RazerS 3, which now supports shared-memory parallelism, an additional seed-based filter with adjustable sensitivity, a much faster, banded version of the Myers' bit-vector algorithm for verification, memory-saving measures and support for the SAM output format. This leads to a much improved performance for mapping reads, in particular, long reads with many errors. We extensively compare RazerS 3 with other popular read mappers and show that its results are often superior to them in terms of sensitivity while exhibiting practical and often competitive run times. In addition, RazerS 3 works without a pre-computed index.
  
  
  METHODS
  Source code and binaries are freely available for download at http://www.seqan.de/projects/razers. RazerS 3 is implemented in C++ and OpenMP under a GPL license using the SeqAn library and supports Linux, Mac OS X and Windows.
authors.affiliation: Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany. david.weese@fu-berlin.de
authors.forename: David
authors.initials: D
authors.lastname: Weese
authors.forename: Manuel
authors.initials: M
authors.lastname: Holtgrewe
authors.forename: Knut
authors.initials: K
authors.lastname: Reinert
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*