SHRiMP2: Sensitive yet Practical Short Read Mapping | Zendy

Matei David | Zendy; Misko Dzamba | Zendy; D. A. LISTER | Zendy; Lucian Ilie | Zendy; Michael Brudno | Zendy

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SHRiMP2: Sensitive yet Practical Short Read Mapping

Author(s) -

Matei David,

Misko Dzamba,

D. A. LISTER,

Lucian Ilie,

Michael Brudno

Publication year - 2011

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btr046

Subject(s) - executable , computer science , shrimp , space (punctuation) , sensitivity (control systems) , source code , code (set theory) , data mining , programming language , biology , operating system , engineering , set (abstract data type) , electronic engineering , fishery

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.

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