Linux cluster

From CSBLwiki

Revision as of 05:28, 12 April 2009 (view source) Csbl (Talk | contribs) (→Programs Installed) ← Older edit		Revision as of 02:41, 16 April 2009 (view source) Csbl (Talk | contribs) (→Programs Installed) Newer edit →
Line 14:		Line 14:
	*de novo		*de novo
-	**edena	+	#de Bruijn graphs
	**velvet		**velvet
		+	**abyss 1.0.5
		+	#suffix tree-based approach
	**QSRA		**QSRA
	**SSAKE		**SSAKE
		+	#overlap-layout-consensus
		+	**edena
		+	#??
	**SHARCGS		**SHARCGS
-	**abyss 1.0.5
	*comparative		*comparative

---

Revision as of 02:41, 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

• • velvet
  • abyss 1.0.5

1. suffix tree-based approach

• • QSRA
  • SSAKE

1. overlap-layout-consensus

• • edena

1. ??

• • 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