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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 originally designed and written by Michael Brudno and Stephen M. Rumble, with considerable input and testing by the SidowLab. Since then, Adrian Dalca, Marc Fiume and Vladimir Yanovsky have made considerable contributions to probability calculations and 2-pass SMS mapping algorithms. Matei David has joined the project with the 1.3.0 release. 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: January 28, 2010 - SHRiMP 1.3.2 is now available. This version fixes a couple of bugs, as explained in HISTORY. We also introduced the '-ungapped' option which tells rmapper to perform ungapped alignment between the queries and the database, as well as a '-M mirna' mode which loads some settings that were tested in the context of micro RNA analysis. For more details, see the README file. (Thank you Alessandro Guffanti.) November 24, 2009 - SHRiMP 1.3.1 is available. This version fixes two bugs. One of them, related to memory management, caused rmapper to allocate more memory than needed, increasing unnecessarily its virtual memory footprint. The other bug caused rmapper to miss some kmers at the beginning of each database sequence (contig). The fix should positively affect the sensitivity of rmapper on databases of small sequences (e.g., miRNA). We'd like to thank Alessandro Guffanti and Hossein Farahani for the detailed feedback that lead to the identification of these bugs. October 6, 2009 - SHRiMP 1.3.0 is now available. As a major upgrade, 'rmapper' now includes proper support for multiple spaced seeds. Using the new default 4 spaced seeds of weight 12 as opposed to the old default of 1 spaced seed of weight 8 decreases the running time by a factor of 5 or even more in certain settings, all without affecting sensitivity. 'rmapper' now comes equipped with several pre-defined sets of parameters, designed for different (approximate) read lengths (see the description of the '-M' option in the README file). June 30, 2009 - SHRiMP 1.2.1 is out. This update primarily includes support for multiple spaced seeds and 'shrimp_var', a new utility for detailing the variations detected for specific hits. Many minor bug fixes and features were added, including the -T and -U flags for rmapper (see the README). Please note that all default Smith-Waterman parameters were divided by 10 in this release in order to accomodate longer reads in our vectorized filter. The algorithms are unchanged, but the alignment scores will by off by an order compared to previous versions. Check out the HISTORY file for more information on changes in this release. For those interested in SHRiMP's inner workings, we have a recent publication in PLoS Computational Biology. February 27, 2009 - SHRiMP 1.2.0 has been released. This version incorporates a mate-pair version of probcalc, substantial bug fixes and enhancements to probcalc, Solaris support, significantly reduced memory usage in rmapper, and support for long spaced seeds up to 128 positions in length. As usual, check the HISTORY file for more information. New features are documented in the README. July 19, 2008 - Concurrent with the ISMB Short-SIG, we're pleased to announce the release of SHRiMP 1.1.0. This release features a number of important changes, namely the addition of an experimental aligner for Helicos 2-pass reads, significant improvements and bugfixes in probcalc, a new, more concise output format with succinct edit string alignment representations, speed enhancements and a number of bugfixes. As always, check out the HISTORY file for more information. Source and ICC builds for Linux (x86 and x86_64) are available for download. OS X builds should be appearing shortly. 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). |