SHRiMP2: sensitive yet practical SHort Read Mapping |
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Authors: | David Matei Dzamba Misko Lister Dan Ilie Lucian Brudno Michael |
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Affiliation: | Department of Computer Science, Princeton University, USA. |
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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. AVAILABILITY: SHRiMP2 executables and source code are freely available at: http://compbio.cs.toronto.edu/shrimp/. |
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