Consed: Difference between revisions
Jump to navigation
Jump to search
Moskalenko (talk | contribs) Created page with "Category:SoftwareCategory:BioinformaticsCategory:Genomics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|consed}} |{{#vardefine:url|http://bozeman.mbt.washington...." |
No edit summary |
||
| (10 intermediate revisions by 3 users 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 19: | Line 19: | ||
<!--Description--> | <!--Description--> | ||
{{#if: {{#var: url}}| | {{#if: {{#var: url}}| | ||
{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
The programs Phrap, Cross_match, and Phred are the leading programs for base | The programs Phrap, Cross_match, and Phred are the leading programs for base | ||
calling, sequence comparisons, and sequence assembly. Phred, Cross_match, | calling, sequence comparisons, and sequence assembly. Phred, Cross_match, | ||
| Line 26: | Line 27: | ||
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. | 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. | ||
<!--Modules--> | <!--Modules--> | ||
==Environment Modules== | |||
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |||
==System Variables== | |||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | |||
<!--Run--> | <!--Run--> | ||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY | DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY | ||
| Line 47: | Line 46: | ||
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
<!--Policy--> | <!--Policy--> | ||
{{#if: {{#var: policy}}|==Usage | {{#if: {{#var: policy}}|==Usage Policy== | ||
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used) | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used) | ||
|}} | |}} | ||
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