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mrFAST: Micro Read Fast Alignment Search Tool

http://mrfast.sourceforge.net/manual.html

mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold, including indels up to 4+4 bp. This manual, describes how to choose the parameters and tune mrFAST with respect to the library settings. mrFAST is designed to find 'all'  mappings for a given set of reads, however it can return one "best" map location if the relevant parameter is invoked.

More at http://mrfast.sourceforge.net/manual.html