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.