[Cdd-commits] r706 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Sat Apr 12 06:56:49 2008
New Revision: 706

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


Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Sat Apr 12 06:56:49 2008
@@ -1198,6 +1198,39 @@
  modular open-source framework for assembly development.
 Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
 
+Depends: minimus
+Homepage: http://amos.sourceforge.net/docs/pipeline/minimus.html
+License: Artistic
+Pkg-Description: AMOS lightweight assembler
+ minimus is an assembly pipeline designed specifically for small
+ data-sets, such as the set of reads covering a specific gene. Note
+ that the code will work for larger assemblies (we have used it to
+ assemble bacterial genomes), however, due to its stringency, the
+ resulting assembly will be highly fragmented. For large and/or
+ complex assemblies the execution of Minimus should be followed by
+ additional processing steps, such as scaffolding.
+ .
+ minimus follows the Overlap-Layout-Consensus paradigm and consists of three main modules:
+  * overlapper - computes the overlaps between the reads using a
+    modified version of the Smith-Waterman local alignment algorithm 
+  * tigger - uses the read overlaps to generate the layouts of reads
+    representing individual contigs 
+  * make-consensus - refines the layouts produced by the tigger to
+    generate accurate multiple alignments within the reads
+ .
+ minimus 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.
+ .
+ minimus is part of the AMOS package - a collaborative effort to
+ develop a modular open-source framework for assembly development.
+Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
+
 Ignore: catissuecore
 Homepage: https://cabig.nci.nih.gov/tools/catissuecore
 License: to be clarified, NCICB Open Source Project Site