[Cdd-commits] r699 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Thu Apr 10 06:56:39 2008
New Revision: 699

Modified:
   projects/med/trunk/debian-med/tasks/bio
Log:
Added mummergpu


Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Thu Apr 10 06:56:39 2008
@@ -1097,3 +1097,30 @@
  The reference to SMILE is made here especially because there is some
  work done in the Debian Med SVN at
  http://svn.debian.org/wsvn/debian-med/trunk/packages/smile/trunk/?rev=0&sc=0
+
+Depends: mummergpu
+Homepage: http://mummergpu.sourceforge.net/
+License: Artistic
+Pkg-Description: High-throughput sequence alignment using Graphics Processing Units
+ The recent availability of new, less expensive high-throughput DNA
+ sequencing technologies has yielded a dramatic increase in the volume
+ of sequence data that must be analyzed. These data are being
+ generated for several purposes, including genotyping, genome
+ resequencing, metagenomics, and de novo genome assembly
+ projects. Sequence alignment programs such as MUMmer have proven
+ essential for analysis of these data, but researchers will need ever
+ faster, high-throughput alignment tools running on inexpensive
+ hardware to keep up with new sequence 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. MUMmerGPU is a GPGPU drop-in
+ replacement for MUMmer, using the GPUs in common workstations to
+ simultaneously 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 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.