SHRiMP2: sensitive yet practical SHort Read Mapping

Bioinformatics. 2011 Apr 1;27(7):1011-2. doi: 10.1093/bioinformatics/btr046. Epub 2011 Jan 28.


We report on a major update (version 2) of the original SHort Read Mapping Program (SHRiMP). SHRiMP2 primarily targets mapping sensitivity, and is able to achieve high accuracy at a very reasonable speed. SHRiMP2 supports both letter space and color space (AB/SOLiD) reads, enables for direct alignment of paired reads and uses parallel computation to fully utilize multi-core architectures.

Availability: SHRiMP2 executables and source code are freely available at:

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Chromosome Mapping*
  • Genomics / methods*
  • Polymorphism, Genetic
  • Sequence Alignment
  • Sequence Analysis, DNA*
  • Software*