[Blends-commit] r2970 - /projects/med/trunk/debian-med/tasks/bio

Mon Oct 10 20:16:08 UTC 2011

Author: tille
Date: Mon Oct 10 20:16:08 2011
New Revision: 2970

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2970
Log:
Added Jellyfish

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

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=2970&op=diff
==============================================================================

--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Mon Oct 10 20:16:08 2011
@@ -3790,6 +3790,30 @@
   * Hybrid direct/tau-leaping.
   * ODE integration.
 
+Depends: jellyfish
+License: GPL-3+
+Homepage: http://www.cbcb.umd.edu/software/jellyfish/
+WNPP: 644925
+Responsible: Shaun Jackman <sjackman at gmail.com>
+Pkg-Description: count k-mers of DNA
+ JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
+ DNA. A k-mer is a substring of length k, and counting the occurrences
+ of all such substrings is a central step in many analyses of DNA
+ sequence. JELLYFISH can count k-mers using an order of magnitude less
+ memory and an order of magnitude faster than other k-mer counting
+ packages by using an efficient encoding of a hash table and by
+ exploiting the "compare-and-swap" CPU instruction to increase
+ parallelism.
+ .
+ JELLYFISH is a command-line program that reads FASTA and multi-FASTA
+ files containing DNA sequences. It outputs its k-mer counts in an
+ binary format, which can be translated into a human-readable text
+ format using the "jellyfish dump" command.
+Published-Title: A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
+Published-Authors: Guillaume Marcais and Carl Kingsford
+Published-In: Bioinformatics
+Published-Year: 2011
+Published-DOI: 10.1093/bioinformatics/btr011
 
 Comment: Several related R packages are listed at CRAN:
          http://cran.r-project.org/web/views/Genetics.html


