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+MUMmerGPU 1.0
+August 7, 2007
+Michael Schatz, Cole Trapnel, Art Delcher, & Amitabh Varshney
+-------------------------------------------------------------
+MUMmerGPU is a high-throughput DNA exact sequence alignment program that
+runs on nVidia G80-class GPUs. It aligns sequences in parallel on the video
+card to achieve a more than 3-fold speedup over the widely used serial CPU
+program MUMmer. It is supports many of the same options as MUMmer, and in
+many cases, can be used as a drop in replacement.
+
+MUMmerGPU uses the "Compute Unified Device Architecture" (CUDA) Software
+development kit to program the graphics cards. If you do not have a nVidia
+G80, you can still use MUMmerGPU using the G80 emulator available in CUDA.
+The emulated version with run much slower than the native version, and
+potentially slower than the CPU version of MUMmer.
+
+Table of Contents
+-----------------
+. Build & Usage Instructions
+. FAQ
+. Acknowledgements
+
+
+
+
+Build & Usage Instructions
+------------------
+1) Download and install the CUDA Toolkit 1.0 for your OS from: 
+   http://developer.nvidia.com/object/cuda.html
+
+2) Download and install the Linux display driver (100.14) from:
+   http://developer.nvidia.com/object/cuda.html
+
+3) Edit the CUDA_INSTALL_PATH in the src/Makefile to point to the top level
+   directory where you installed the CUDA Toolkit.
+
+4) Run 'make' in the src directory, which will compile the program to run on
+   the GPU as:
+   bin/linux32/release/mummergpu
+
+   If you do not have a G80, you can also run 'make emu=1' which will compile
+   the program to run on the CPU with an emulator as:
+   bin/linux32/emurelease/mummergpu
+
+5) Usage: mummergpu [options] reference.fa query.fa
+   reference.fa must be a single sequence in fasta format
+   query.fa is a multi-fasta file containing your sequences the more
+   sequences you provide, the faster MUMmerGPU will execute.
+   See mummergpu -h for an explanation of the options, many of the options are
+   the same as those available in MUMmer.
+   See: http://mummer.sourceforge.net/manual/#mummer for more information
+
+
+FAQs
+----
+Q: I have a G70 or other older nVidia graphics card. Can I run MUMmerGPU on it?
+
+A: No, MUMmerGPU requires a G80 or later video card. You can run MUMmerGPU
+with the G80 emulator, but the alignments will be computed much slower than
+if you had a G80.
+
+
+
+Q: How does MUMmerGPU handle the MUMmer uniqueness options: -mum, -mumcand,
+-mumreference, and -maxmatch?  
+
+A: MUMmerGPU does not filter matches by uniques and always computes all
+maximal matches regardless of their uniqueness (-maxmatch). The filtering
+options provided by MUMmer (-mum, -mumcand, & -mumreference) are heuristics to
+speed up the alignment process. This is not necessary with the very efficient
+MUMmerGPU. If you want to filter your alignments to report only the most
+biologically significant, you should use 'delta-filter' instead, which uses a
+more sophisticated algorithm for finding the best set of alignments.
+
+See the MUMmer manual for more information: 
+http://mummer.sourceforge.net/manual/#filter
+
+
+Q: How does MUMmerGPU handle ambiguous bases?
+
+A: MUMmerGPU only supports DNA characters (ACGT). Non DNA characters in the
+reference are converted arbitrarily to a DNA character (A). Non-DNA characters
+in the query set are converted to 'x' to guarantee a mis-match.
+
+
+Q: How can I get help with MUMmerGPU?
+
+A: Subscribe and post to the mailing list at: 
+   http://sourceforge.net/mail/?group_id=201280
+
+
+
+
+Acknowledgements
+----------------
+This work was supported in part by National Institutes of Health grants
+R01-LM006845 and R01-LM007938, and National Science Foundation CISE RI grant
+CNS 04-03313.
+