Difference between revisions of "Consed"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
|||
| (One intermediate revision by the same user not shown) | |||
| Line 1: | Line 1: | ||
| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Genomics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|consed}} | |{{#vardefine:app|consed}} | ||
| Line 29: | Line 29: | ||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | |||
| − | |||
| − | < | ||
==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__ | ||
| − | |||
| − | |||
Latest revision as of 18:39, 12 August 2022
Description
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