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SHort Read Mapping Program SHRiMP

Alternative name: SHRiMP2

Allows to align genomic reads against a target genome. SHRiMP primarily targets mapping accuracy, enabling the alignment of reads with extensive polymorphism and sequencing errors. The software supports Illumina/Solexa, Roche/454 and AB/SOLiD reads, a paired mapping mode, parameters for miRNA mapping, and parallel computation. Its speed was evaluated on real AB SOLiD data.

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SHRiMP forum

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SHRiMP classification

SHRiMP specifications

Software type:
Restrictions to use:
Input format:
Operating system:
Unix/Linux, Mac OS
Source code URL:
Command line interface
Input data:
The reads and the genome files.
Output format:
Computer skills:

SHRiMP distribution


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SHRiMP support


  • Matei David <>


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Department of Computer Science, Princeton University, Princeton, NJ, USA; Department of Computer Science, University of Toronto, Toronto, ON, USA; Department of Computer Science, University of Western Ontario and Donnelly Centre, University of Toronto, Toronto, ON, USA

Funding source(s)

Supported by MITACS, CIHR, and Life Technologies research grants, NSF grant (CCF-0832797).

Link to literature

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