[Cdd-commits] r701 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Thu Apr 10 12:29:19 2008
New Revision: 701

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


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 12:29:19 2008
@@ -1166,3 +1166,31 @@
  and improve in hopes of eventually becoming a widely accepted and
  deployed assembly infrastructure. In this sense, AMOS is both a
  design philosophy and a software system.
+
+Depends: amoscmp
+Homepage: http://amos.sourceforge.net/docs/pipeline/AMOScmp.html
+License: Artistic
+Pkg-Description: comparative genome assembly package
+ A comparative assembler is a program that can assemble a set of
+ shotgun reads from an organism by mapping them to the finished
+ sequence of a related organism. Thus, a comparative assembler
+ transforms the traditional overlap-layout-consensus approach to
+ alignment-layout-consensus. The AMOScmp package uses the MUMmer
+ program to perform a mapping of the reads to the reference genome,
+ then processes the alignment results with a sophisticated layout
+ program designed to take into account polymorphisms between the two
+ genomes. For a detailed description of the algorithms involved please
+ refer to the paper listed in the References section.
+ .
+ AMOScmp uses as AMOS messages as both the inputs and the outputs (see
+ documentation). Two utilities are provided to process these files:
+ tarchive2amos - a versatile converter from trace archive .seq, .qual,
+ and .xml information into AMOS formatted data; amos2ace - a converter
+ from AMOS formatted data to the .ACE assembly format. In addition,
+ the AMOS::AmosLib Perl module is provided as a tool for users who
+ prefer to write their own conversion utilities. Please see the
+ documentation included with the distribution for more information.
+ .
+ AMOScmp is part of the AMOS package (see
+ http://amos.sourceforge.net/)- a collaborative effort to develop a
+ modular open-source framework for assembly development.