SHRiMP2: Sensitive yet Practical Short Read Mapping Academic Article uri icon

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  • Abstract Summary: 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: Contact: Supplementary information:  Supplementary data are available at Bioinformatics online.


  • David, Matei
  • Dzamba, Misko
  • Lister, Dan
  • Ilie, Lucian
  • Brudno, Michael

publication date

  • April 1, 2011