Difference between revisions of "CAP3"

Latest revision as of 13:19, 15 August 2022

CAP3 is a sequence assembly program.

Intel processor optimized versions of cap3 and formcon are installed at HPC.

Opteron optimized versions of these binaries are named cap3-opteron and formcon-opteron.

In addition, pcap binaries are also provided.

Run module spider cap3 to find out what environment modules are available for this application.

@@ Line 1: / Line 1: @@
 __NOTOC__
 __NOEDITSECTION__
-[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
+[[Category:Software]][[Category:Biology]][[Category:Assembly]]
 {|
 <!--Main settings - REQUIRED-->
@@ Line 20: / Line 20: @@
 {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
-CAP3 is a sequence assembly program. See documentation at [http://deepc2.psi.iastate.edu/aat/cap/capdoc.html capdoc site].
+CAP3 is a sequence assembly program.
 Intel processor optimized versions of cap3 and formcon are installed at HPC.
@@ Line 27: / Line 27: @@
 In addition, pcap binaries are also provided.
-<!-- -->
+<!--Modules-->
-==Required Modules==
+==Environment Modules==
-[[Modules|modules documentation]]
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-===Serial===
-*{{#var:app}}
 ==System Variables==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 * HPC_CAP3_BIN - location of the CAP3 executables directory
 * HPC_CAP3_DOC - location of the CAP3 docs directory