[Blends-commit] r2013 - projects/med/trunk/debian-med/tasks

[Debian Pure Blends Subversion Commit]

Author: plessy
Date: Thu Nov 26 00:56:14 2009
New Revision: 2013
URL: http://svn.debian.org/viewsvn/blends?rev=2013&view=rev

Log:
Added bowtie and crossbow.


Modified:
   projects/med/trunk/debian-med/tasks/bio

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/viewsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=2013&view=diff&r1=2013&r2=2012&p1=projects/med/trunk/debian-med/tasks/bio&p2=projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Thu Nov 26 00:56:14 2009
@@ -3184,3 +3184,27 @@
 
 Comment: Several related R packages are listed at CRAN:
          http://cran.r-project.org/web/views/Genetics.html
+
+Depends: bowtie
+Homepage: http://bowtie-bio.sourceforge.net/
+License: Artistic
+X-Category: Sequencing
+Pkg-Description: An ultrafast memory-efficient short read aligner
+ Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short
+ DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
+ reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep
+ its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB
+ for paired-end).
+
+Depends: crossbow
+Homepage: http://bowtie-bio.sourceforge.net/crossbow
+License: Artistic
+X-Category: Sequencing
+Pkg-Description: Genotyping from short reads using cloud computing
+ Crossbow is a scalable software pipeline for whole genome resequencing
+ analysis. It combines Bowtie, an ultrafast and memory efficient short read
+ aligner, and SoapSNP, an accurate genotyper, within Hadoop to distribute and
+ accelerate the computation with many nodes. The pipeline can accurately analyze
+ over 35x coverage of a human genome in one day on a 10-node local cluster, or
+ in 3 hours for about $100 using a 40-node, 320-core cluster rented from
+ Amazon's EC2 utility computing service.