Linux cluster

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Revision as of 02:41, 16 April 2009 (view source) Csbl (Talk | contribs) (→Programs Installed) ← Older edit		Revision as of 02:42, 16 April 2009 (view source) Csbl (Talk | contribs) (→Programs Installed) Newer edit →
Line 15:		Line 15:
	*de novo		*de novo
	#de Bruijn graphs		#de Bruijn graphs
-	**velvet	+	##velvet
-	**abyss 1.0.5	+	##abyss 1.0.5
	#suffix tree-based approach		#suffix tree-based approach
-	**QSRA	+	##QSRA
-	**SSAKE	+	##SSAKE
	#overlap-layout-consensus		#overlap-layout-consensus
-	**edena	+	##edena
	#??		#??
	**SHARCGS		**SHARCGS

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Revision as of 02:42, 16 April 2009

Programs Installed

Bin directory (/home/tools)

• Statistical Packages
  • R-2.8.1
• assembly packages
  • amos
  • EMBOSS(/usr/local/share/EMBOSS)
  • EULER ( ?? )

• ab initio assembly
  • ARACHNE 3.2
  • WGS

• de novo

1. de Bruijn graphs
   1. velvet
   2. abyss 1.0.5
2. suffix tree-based approach
   1. QSRA
   2. SSAKE
3. overlap-layout-consensus
   1. edena
4. ??

• • SHARCGS

• comparative
  • maq 0.7.1

• realigner
• SOAPaligner

• manatee(requir setting DIR)
• iprscan
• BLAST

Modules

• Python modules
  • biopython
  • pyrex
  • numpy
  • Rpy ( RHOME problem)
• Perl modules