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About: SHRiMP is a software package for aligning genomic reads against a target genome. It was primarily developed with the multitudinous short reads of next generation sequencing machines in mind, as well as Applied Biosystem's colourspace genomic representation. SHRiMP was designed and written by Michael Brudno and Stephen M. Rumble, with considerable input and testing by the SidowLab. The authors may be contacted via e-mail at: shrimp at cs.toronto.edu. Additional information is available in the README file. |
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News: March 25, 2008 - SHRiMP 1.0.5 is out. Bug fixes included better handling of input files with strange characters (e.g. MSDOS newlines), proper wobble code complementation, and some GCC 4 compiler warning fixes. Default parameters have changed slightly: letter space seeds were increased to better deal with longer reads of 454 and Illumina/Solexa machines, kmer pruning is disabled by default again, and gap open and crossover penalties were increased. A new feature for better handling non-uniform read lengths has been added as well: the -h, -v and -w flags can now take relative arguments. For example, '-w 120%' specifies a window size to be 120% of each read's length. Please read the HISTORY file for more information. January 24, 2008 - SHRiMP 1.0.4 is now available (1.0.3 was an internal development version). Some important bug fixes were made regarding colourspace alignment and various useful usability features were added. Please read the HISTORY file for more information. November 6, 2007 - SHRiMP 1.0.2 is now available. An incorrect assertion bug has been fixed and various documentation updates were made. November 2, 2007 - SHRiMP 1.0.1, the first public release, is now available. Use the links on the left to download in source form, or pre-compiled static binaries for i686 and x86_64 platforms (Linux 2.6). |