Difference between revisions of "Consed"

From UFRC
Jump to navigation Jump to search
m (Text replacement - "#uppercase" to "uc")
Line 29: Line 29:
  
 
<!--Modules-->
 
<!--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}}
 
<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
 
 
==System Variables==
 
==System Variables==
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
Line 68: Line 65:
 
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
 
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
 
__NOTOC____NOEDITSECTION__
 
__NOTOC____NOEDITSECTION__
=Validation=
 
* Validated 4/5/2018
 

Revision as of 17:27, 10 June 2022

Description

consed website  

The programs Phrap, Cross_match, and Phred are the leading programs for base calling, sequence comparisons, and sequence assembly. Phred, Cross_match, and Phrap are currently used in many large-scale DNA sequencing and mutation detection projects in academic and biotech settings.

Consed/Autofinish is a tool for viewing, editing, and finishing sequence assemblies created with phrap. Finishing capabilities include allowing the user to pick primers and templates, suggesting additional sequencing reactions to perform, and facilitating checking the accuracy of the assembly using digest and forward/reverse pair information.

Environment Modules

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

System Variables

  • HPC_CONSED_DIR - installation directory