title: SHRiMP2: sensitive yet practical SHort Read Mapping.
abstract: 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.
  
  
  BACKGROUND
  SHRiMP2 executables and source code are freely available at: http://compbio.cs.toronto.edu/shrimp/.
authors.affiliation: Department of Computer Science, Princeton University, USA.
authors.forename: Matei
authors.initials: M
authors.lastname: David
authors.forename: Misko
authors.initials: M
authors.lastname: Dzamba
authors.forename: Dan
authors.initials: D
authors.lastname: Lister
authors.forename: Lucian
authors.initials: L
authors.lastname: Ilie
authors.forename: Michael
authors.initials: M
authors.lastname: Brudno
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping; D023281:Genomics / Q000379:methods*; D011110:Polymorphism, Genetic; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software