MUMmerGPU modified by Michael Schatz

Michael Schatz — Tue, 20 May 2014 20:03:47 -0000

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-Welcome to your wiki!
+**MUMmerGPU: High-throughput sequence alignment using Graphics Processing Units.**  
+[Michael Schatz](http://schatzlab.cshl.edu) and [Cole Trapnell](http://www.cbcb.umd.edu/~cole/)  
+[Center for Bioinformatics and Computational Biology](http://www.cbcb.umd.edu), [University of Maryland](http://www.umd.edu)

-This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].

-The wiki uses [Markdown](/p/mummergpu/wiki/markdown_syntax/) syntax.
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+MUMmerGPU is an open-source high-throughput parallel pairwise local sequence alignment program that runs on commodity Graphics Processing Units (GPUs) in common workstations. MUMmerGPU uses the new Compute Unified Device Architecture (CUDA) from nVidia to align multiple query sequences against a single reference sequence stored as a suffix tree. By processing the queries in parallel on the highly parallel graphics card, MUMmerGPU achieves more than a 10-fold speedup over a serial CPU version of the sequence alignment kernel, and outperforms the exact alignment component of MUMmer on a high end CPU by 3.5-fold in total application time when aligning reads from recent sequencing projects using Solexa/Illumina, 454, and Sanger sequencing technologies. MUMmerGPU is a low cost, ultra-fast sequence alignment program designed to handle the increasing volume of data produced by new, high-throughput sequencing technologies. 

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+[BMC Bioinformatics 2007 8:474](http://www.biomedcentral.com/1471-2105/8/474/abstract)
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+MUMmerGPU 2.0 features a new stackless depth-first-search print kernel and is 13x faster than the serial CPU version of the alignment code and nearly 4x faster in total computation time than MUMmerGPU 1.0. We exhaustively examined 128 GPU data layout configurations to improve register footprint and running time and conclude higher occupancy has greater impact than reduced latency for achieving high performance for data intensive GPGPU applications. 
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+[Parallel Computing 2009 35(8-9)429-440](http://dx.doi.org/10.1016/j.parco.2009.05.002)
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+See the [Tesla Bio Workbench](http://www.nvidia.com/object/mummer_on_tesla.html) page for up to date results. 
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+
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+## Announcements
+
+  * Nov 8, 2010 - MUMmerGPU workloads [download](ftp://ftp.cbcb.umd.edu/pub/data/mschatz/mummergpu/mummergpu20-workloads.tgz)
+  * Feb 21, 2010 - Add link to Tesla Bio Workbench 
+  * Jan 19, 2010 - MUMmerGPU 2.0 official release 
+  * Nov 13, 2009 - Moved to a Wiki 
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+  
+
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+## Links
+
+  * [Project Page](http://sourceforge.net/projects/mummergpu/)
+  * [Downloads](http://sourceforge.net/projects/mummergpu/files/)
+  * [Tesla Bio Workbench](http://www.nvidia.com/object/mummer_on_tesla.html)
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+  
+
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+## Related Links
+
+  * [Bowtie](http://bowtie-bio.sf.net) An ultrafast memory-efficient short read aligner 
+  * [CloudBurst](http://cloudburst-bio.sf.net) Highly Sensitive Short Read Mapping with MapReduce 
+  * [Crossbow](http://bowtie-bio.sf.net/crossbow) Whole Genome Resequencing Analysis in the Clouds

Home modified by Michael Schatz

Michael Schatz — Tue, 20 May 2014 20:03:20 -0000

Welcome to your wiki!

This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].

The wiki uses Markdown syntax.

Project Members:

Cole Trapnell (admin)
Michael Schatz (admin)

Recent changes to MUMmerGPU

MUMmerGPU modified by Michael Schatz

Home modified by Michael Schatz

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